{ "metadata": { "name": "", "signature": "sha256:a98f052fcee22055c5f074f0f5019598abad627681083e154ffe2ee1c6e4c723" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "code", "collapsed": false, "input": [ "from IPython.display import HTML\n", "import pandas as pd\n", "import numpy as np\n", "import os\n", "import matplotlib.pyplot as plt\n", "from matplotlib_venn import venn3, venn3_circles, venn3_unweighted\n", "import seaborn\n", "%pylab inline" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Populating the interactive namespace from numpy and matplotlib\n" ] } ], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "#These are defined by the way annovar defines precedence. I found empirically that stop_gain > frame_shift in annovar, hence the reverse\n", "precedence_dict = {\n", "\"splicing_variant\": 1,\n", "\"frameshift_variant\": 4,\n", "\"stop_gained\": 2,\n", "\"stop_lost\": 3,\n", "\"inframe_variant\": 5,\n", "\"nonsynonymous_variant\": 6,\n", "\"synonymous_variant\": 7,\n", "\"5_prime_UTR_variant\": 8,\n", "\"3_prime_UTR_variant\": 9,\n", "\"intron_variant\": 10,\n", "\"upstream_gene_variant\": 11,\n", "\"downstream_gene_variant\": 12,\n", "\"intergenic_variant\": 13,\n", "\"intron_variant\": 14,\n", "\"upstream_gene_variant\": 15,\n", "\"regulatory_region_variant\": 16,\n", "\"ignored\": 17\n", "}\n", "\n", "def ranked(col):\n", " return max(col, key=lambda val: -1*precedence_dict[val])" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 2 }, { "cell_type": "code", "collapsed": true, "input": [ "with pd.get_store('classified_variant_store.h5') as store:\n", " snpeff_subset = store.get(\"cftr_snpeff_ensembl_subset\")\n", "ensembl_symbol_mapping = {\"CFTR\":\"ENSG00000001626\",\n", " \"AC000111.3\": \"ENSG00000232661\",\n", " \"AC000111.4\":\"ENSG00000237974\",\n", " \"AC000111.5\": \"ENSG00000234001\",\n", " \"AC000111.6\": \"ENSG00000083622\", \n", " \"CTTNBP2\": \"ENSG00000077063\",\n", " \"\":\"\"}\n", "snpeff_subset[\"EnsemblGene\"] = snpeff_subset[\"Gene_Name\"].apply(lambda x: ensembl_symbol_mapping[x])\n", "grouped_snpeff_subset = snpeff_subset.groupby([\"EnsemblGene\", \"POS\", \"REF\", \"ALT\"])\n", "grouped_snpeff_subset = grouped_snpeff_subset.agg({\"normalized_so_snpeff\": ranked})\n", "grouped_snpeff_subset = grouped_snpeff_subset.rename(columns={\"normalized_so_snpeff\": \"normalized_so_snpeff_max\"}).reset_index()\n", "grouped_snpeff_subset = pd.merge(grouped_snpeff_subset, snpeff_subset, how=\"left\", on=[\"POS\", \"REF\", \"ALT\", \"EnsemblGene\"])\n", "grouped_snpeff_subset = grouped_snpeff_subset[grouped_snpeff_subset[\"normalized_so_snpeff_max\"] == grouped_snpeff_subset[\"normalized_so_snpeff\"]]\n", "#kludge ties are broken by taking the first element in the group (ie randomly; this should only really effect the transcript level comparisons, ie hgvs etc)\n", "grouped_snpeff_subset = grouped_snpeff_subset.groupby([\"EnsemblGene\", \"POS\", \"REF\", \"ALT\"]).first()\n", "agg_snpeff = grouped_snpeff_subset.reset_index()\n", "del agg_snpeff[\"normalized_so_snpeff_max\"]\n", "del grouped_snpeff_subset\n", "del snpeff_subset\n", "agg_snpeff.rename(columns={\"EnsemblGene\":\"Gene\"}, inplace=True)\n", "agg_snpeff[100000:100050]" ], "language": "python", "metadata": {}, "outputs": [ { "html": [ "
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "
---|---|---|---|---|---|---|---|---|---|---|
100000 | \n", "ENSG00000001626 | \n", "117235027 | \n", "C | \n", "G | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Thr784Arg/c.2351C>G | \n", "nonsynonymous_variant | \n", "
100001 | \n", "ENSG00000001626 | \n", "117235027 | \n", "C | \n", "T | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Thr784Ile/c.2351C>T | \n", "nonsynonymous_variant | \n", "
100002 | \n", "ENSG00000001626 | \n", "117235027 | \n", "CA | \n", "C | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X784X/c.2352*>-A | \n", "frameshift_variant | \n", "
100003 | \n", "ENSG00000001626 | \n", "117235027 | \n", "CAT | \n", "C | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X784X/c.2352*>-AT | \n", "frameshift_variant | \n", "
100004 | \n", "ENSG00000001626 | \n", "117235027 | \n", "CATG | \n", "C | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_DELETION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X784Thr/c.2352*>-ATG | \n", "inframe_variant | \n", "
100005 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "AA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+A | \n", "frameshift_variant | \n", "
100006 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "AATC | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+ATC | \n", "inframe_variant | \n", "
100007 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "AC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+C | \n", "frameshift_variant | \n", "
100008 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "ACA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+CA | \n", "frameshift_variant | \n", "
100009 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "ACAG | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+CAG | \n", "inframe_variant | \n", "
100010 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "ACG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+CG | \n", "frameshift_variant | \n", "
100011 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "AG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+G | \n", "frameshift_variant | \n", "
100012 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "AT | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>+T | \n", "frameshift_variant | \n", "
100013 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "C | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Thr784Thr/c.2352A>C | \n", "synonymous_variant | \n", "
100014 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "G | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Thr784Thr/c.2352A>G | \n", "synonymous_variant | \n", "
100015 | \n", "ENSG00000001626 | \n", "117235028 | \n", "A | \n", "T | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Thr784Thr/c.2352A>T | \n", "synonymous_variant | \n", "
100016 | \n", "ENSG00000001626 | \n", "117235028 | \n", "AT | \n", "A | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785X/c.2353*>-T | \n", "frameshift_variant | \n", "
100017 | \n", "ENSG00000001626 | \n", "117235028 | \n", "ATG | \n", "A | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785X/c.2353*>-TG | \n", "frameshift_variant | \n", "
100018 | \n", "ENSG00000001626 | \n", "117235028 | \n", "ATGG | \n", "A | \n", ". | \n", "CODON_DELETION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2353*>-TGG | \n", "inframe_variant | \n", "
100019 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "A | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785Arg/c.2353T>A | \n", "nonsynonymous_variant | \n", "
100020 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "C | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785Arg/c.2353T>C | \n", "nonsynonymous_variant | \n", "
100021 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "G | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785Gly/c.2353T>G | \n", "nonsynonymous_variant | \n", "
100022 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TA | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785*/c.2354*>+A | \n", "stop_gained | \n", "
100023 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2354*>+C | \n", "frameshift_variant | \n", "
100024 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2354*>+G | \n", "frameshift_variant | \n", "
100025 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TGCT | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2354*>+GCT | \n", "inframe_variant | \n", "
100026 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TT | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2354*>+T | \n", "frameshift_variant | \n", "
100027 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TTC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2354*>+TC | \n", "frameshift_variant | \n", "
100028 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TTG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2354*>+TG | \n", "frameshift_variant | \n", "
100029 | \n", "ENSG00000001626 | \n", "117235029 | \n", "T | \n", "TTGA | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2354*>+TGA | \n", "inframe_variant | \n", "
100030 | \n", "ENSG00000001626 | \n", "117235029 | \n", "TG | \n", "T | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785X/c.2354*>-G | \n", "frameshift_variant | \n", "
100031 | \n", "ENSG00000001626 | \n", "117235029 | \n", "TGG | \n", "T | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785X/c.2354*>-GG | \n", "frameshift_variant | \n", "
100032 | \n", "ENSG00000001626 | \n", "117235029 | \n", "TGGA | \n", "T | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_DELETION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785Tyr/c.2354*>-GGA | \n", "inframe_variant | \n", "
100033 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "A | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785*/c.2354G>A | \n", "stop_gained | \n", "
100034 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "C | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785Ser/c.2354G>C | \n", "nonsynonymous_variant | \n", "
100035 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GA | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785*/c.2355*>+A | \n", "stop_gained | \n", "
100036 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GAT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785*/c.2355*>+AT | \n", "stop_gained | \n", "
100037 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2355*>+C | \n", "frameshift_variant | \n", "
100038 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2355*>+G | \n", "frameshift_variant | \n", "
100039 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GGC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2355*>+GC | \n", "frameshift_variant | \n", "
100040 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GT | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2355*>+T | \n", "frameshift_variant | \n", "
100041 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GTGA | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2355*>+TGA | \n", "inframe_variant | \n", "
100042 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "GTGC | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785X/c.2355*>+TGC | \n", "inframe_variant | \n", "
100043 | \n", "ENSG00000001626 | \n", "117235030 | \n", "G | \n", "T | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785Leu/c.2354G>T | \n", "nonsynonymous_variant | \n", "
100044 | \n", "ENSG00000001626 | \n", "117235030 | \n", "GG | \n", "G | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785X/c.2355*>-G | \n", "frameshift_variant | \n", "
100045 | \n", "ENSG00000001626 | \n", "117235030 | \n", "GGA | \n", "G | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785X/c.2355*>-GA | \n", "frameshift_variant | \n", "
100046 | \n", "ENSG00000001626 | \n", "117235030 | \n", "GGAA | \n", "G | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_DELETION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X785Cys/c.2355*>-GAA | \n", "inframe_variant | \n", "
100047 | \n", "ENSG00000001626 | \n", "117235031 | \n", "G | \n", "A | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785*/c.2355G>A | \n", "stop_gained | \n", "
100048 | \n", "ENSG00000001626 | \n", "117235031 | \n", "G | \n", "C | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Trp785Cys/c.2355G>C | \n", "nonsynonymous_variant | \n", "
100049 | \n", "ENSG00000001626 | \n", "117235031 | \n", "G | \n", "GA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Asn786X/c.2356*>+A | \n", "frameshift_variant | \n", "
50 rows \u00d7 10 columns
\n", "\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "
---|---|---|---|---|---|---|---|---|
80000 | \n", "ENSG00000001626 | \n", "117188850 | \n", "G | \n", "GTC | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426SerfsTer14ENST000004... | \n", "frameshift_variant | \n", "
80001 | \n", "ENSG00000001626 | \n", "117188850 | \n", "G | \n", "GTGA | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Ala425_Val426insTerENST000... | \n", "stop_gained | \n", "
80002 | \n", "ENSG00000001626 | \n", "117188850 | \n", "G | \n", "T | \n", ". | \n", "synonymous_variant | \n", "ENST00000426809.1:c.1275G>T(p.%3D)ENST00000426... | \n", "synonymous_variant | \n", "
80003 | \n", "ENSG00000001626 | \n", "117188850 | \n", "GG | \n", "G | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426LeufsTer13ENST000004... | \n", "frameshift_variant | \n", "
80004 | \n", "ENSG00000001626 | \n", "117188850 | \n", "GGT | \n", "G | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426CysfsTer25ENST000004... | \n", "frameshift_variant | \n", "
80005 | \n", "ENSG00000001626 | \n", "117188850 | \n", "GGTT | \n", "G | \n", ". | \n", "inframe_deletion | \n", "ENSP00000389119.1:p.Val426delENST00000426809.1... | \n", "inframe_variant | \n", "
80006 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "A | \n", ". | \n", "missense_variant | \n", "ENSP00000389119.1:p.Val426IleENST00000426809.1... | \n", "nonsynonymous_variant | \n", "
80007 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "C | \n", ". | \n", "missense_variant | \n", "ENSP00000389119.1:p.Val426LeuENST00000426809.1... | \n", "nonsynonymous_variant | \n", "
80008 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GA | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426AspfsTer26ENST000004... | \n", "frameshift_variant | \n", "
80009 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GAC | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426AspfsTer14ENST000004... | \n", "frameshift_variant | \n", "
80010 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GAGT | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Val426delinsGluPheENST0000... | \n", "inframe_variant | \n", "
80011 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GAT | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426AspfsTer14ENST000004... | \n", "frameshift_variant | \n", "
80012 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GC | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426AlafsTer26ENST000004... | \n", "frameshift_variant | \n", "
80013 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GG | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426GlyfsTer26ENST000004... | \n", "frameshift_variant | \n", "
80014 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GGTA | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Val426delinsGlyIleENST0000... | \n", "inframe_variant | \n", "
80015 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "GT | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ala427CysfsTer25ENST000004... | \n", "frameshift_variant | \n", "
80016 | \n", "ENSG00000001626 | \n", "117188851 | \n", "G | \n", "T | \n", ". | \n", "missense_variant | \n", "ENSP00000389119.1:p.Val426PheENST00000426809.1... | \n", "nonsynonymous_variant | \n", "
80017 | \n", "ENSG00000001626 | \n", "117188851 | \n", "GT | \n", "G | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ala427LeufsTer12ENST000004... | \n", "frameshift_variant | \n", "
80018 | \n", "ENSG00000001626 | \n", "117188851 | \n", "GTT | \n", "G | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Val426GlyfsTer25ENST000004... | \n", "frameshift_variant | \n", "
80019 | \n", "ENSG00000001626 | \n", "117188851 | \n", "GTTG | \n", "G | \n", ". | \n", "inframe_deletion | \n", "ENSP00000389119.1:p.Val426delENST00000426809.1... | \n", "inframe_variant | \n", "
80020 | \n", "ENSG00000001626 | \n", "117188852 | \n", "T | \n", "A | \n", ". | \n", "missense_variant | \n", "ENSP00000389119.1:p.Val426AspENST00000426809.1... | \n", "nonsynonymous_variant | \n", "
80021 | \n", "ENSG00000001626 | \n", "117188852 | \n", "T | \n", "C | \n", ". | \n", "missense_variant | \n", "ENSP00000389119.1:p.Val426AlaENST00000426809.1... | \n", "nonsynonymous_variant | \n", "
80022 | \n", "ENSG00000001626 | \n", "117188852 | \n", "T | \n", "G | \n", ". | \n", "missense_variant | \n", "ENSP00000389119.1:p.Val426GlyENST00000426809.1... | \n", "nonsynonymous_variant | \n", "
23 rows \u00d7 8 columns
\n", "\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|
2000 | \n", "ENSG00000001626 | \n", "117119399 | \n", "GGT | \n", "G | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2001 | \n", "ENSG00000001626 | \n", "117119399 | \n", "GGTA | \n", "G | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2002 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "A | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2003 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "C | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2004 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GA | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2005 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GAGC | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2006 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GC | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2007 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GG | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2008 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GGCA | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2009 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GT | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2010 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GTA | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2011 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "GTG | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2012 | \n", "ENSG00000001626 | \n", "117119400 | \n", "G | \n", "T | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2013 | \n", "ENSG00000001626 | \n", "117119400 | \n", "GT | \n", "G | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2014 | \n", "ENSG00000001626 | \n", "117119400 | \n", "GTA | \n", "G | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2015 | \n", "ENSG00000001626 | \n", "117119400 | \n", "GTAA | \n", "G | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2016 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "A | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2017 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "C | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2018 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "G | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2019 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TA | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2020 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TAT | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2021 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TC | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2022 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TCGT | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2023 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TG | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2024 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TGCT | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2025 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TGT | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2026 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TT | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
2027 | \n", "ENSG00000001626 | \n", "117119401 | \n", "TA | \n", "T | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2028 | \n", "ENSG00000001626 | \n", "117119401 | \n", "TAA | \n", "T | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2029 | \n", "ENSG00000001626 | \n", "117119401 | \n", "TAAA | \n", "T | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2030 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "AA | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2031 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "AAG | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2032 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "AAGT | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2033 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "AC | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2034 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "ACAG | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2035 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "AG | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2036 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "AGT | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2037 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "AT | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2038 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "C | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2039 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "G | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2040 | \n", "ENSG00000001626 | \n", "117119402 | \n", "A | \n", "T | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2041 | \n", "ENSG00000001626 | \n", "117119402 | \n", "AA | \n", "A | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2042 | \n", "ENSG00000001626 | \n", "117119402 | \n", "AAA | \n", "A | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2043 | \n", "ENSG00000001626 | \n", "117119402 | \n", "AAAT | \n", "A | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2044 | \n", "ENSG00000001626 | \n", "117119403 | \n", "A | \n", "AA | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2045 | \n", "ENSG00000001626 | \n", "117119403 | \n", "A | \n", "AC | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2046 | \n", "ENSG00000001626 | \n", "117119403 | \n", "A | \n", "ACAG | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2047 | \n", "ENSG00000001626 | \n", "117119403 | \n", "A | \n", "ACT | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2048 | \n", "ENSG00000001626 | \n", "117119403 | \n", "A | \n", "ACTG | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
2049 | \n", "ENSG00000001626 | \n", "117119403 | \n", "A | \n", "AG | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
50 rows \u00d7 7 columns
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1403 | \n", "ENSG00000001626 | \n", "117105737 | \n", "C | \n", "A | \n", ". | \n", "UPSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | upstream_gene_variant | \n", ". | \n", "upstream_gene_variant | \n", "\n", " | upstream_gene_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
1404 | \n", "ENSG00000001626 | \n", "117105737 | \n", "C | \n", "CA | \n", ". | \n", "UPSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | upstream_gene_variant | \n", ". | \n", "upstream_gene_variant | \n", "\n", " | upstream_gene_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
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1406 | \n", "ENSG00000001626 | \n", "117105737 | \n", "C | \n", "CC | \n", ". | \n", "UPSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | upstream_gene_variant | \n", ". | \n", "upstream_gene_variant | \n", "\n", " | upstream_gene_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
1407 | \n", "ENSG00000001626 | \n", "117105737 | \n", "C | \n", "CCTG | \n", ". | \n", "UPSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | upstream_gene_variant | \n", ". | \n", "upstream_gene_variant | \n", "\n", " | upstream_gene_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
14148 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2814 | \n", "ENSG00000001626 | \n", "117105837 | \n", "TT | \n", "T | \n", ". | \n", "EXON | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | ignored | \n", ". | \n", "non_coding_exon_variant | \n", "ENST00000546407.1:n.1delT | \n", "ignored | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
2815 | \n", "ENSG00000001626 | \n", "117105837 | \n", "TTG | \n", "T | \n", ". | \n", "EXON | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | ignored | \n", ". | \n", "non_coding_exon_variant | \n", "ENST00000546407.1:n.1_2delTG | \n", "ignored | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
2816 | \n", "ENSG00000001626 | \n", "117105837 | \n", "TTGA | \n", "T | \n", ". | \n", "EXON | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | ignored | \n", ". | \n", "non_coding_exon_variant | \n", "ENST00000546407.1:n.1_3delTGA | \n", "ignored | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
2817 | \n", "ENSG00000001626 | \n", "117105838 | \n", "T | \n", "A | \n", ". | \n", "EXON | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | ignored | \n", ". | \n", "non_coding_exon_variant | \n", "ENST00000546407.1:n.1T>A | \n", "ignored | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
2818 | \n", "ENSG00000001626 | \n", "117105838 | \n", "T | \n", "C | \n", ". | \n", "EXON | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | ignored | \n", ". | \n", "non_coding_exon_variant | \n", "ENST00000546407.1:n.1T>C | \n", "ignored | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
661 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3460 | \n", "ENSG00000001626 | \n", "117105883 | \n", "AAGG | \n", "A | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | splicing_variant | \n", ". | \n", "splice_donor_variant | \n", "ENST00000546407.1:n.47_48+1delAGG | \n", "splicing_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3473 | \n", "ENSG00000001626 | \n", "117105884 | \n", "AGG | \n", "A | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | splicing_variant | \n", ". | \n", "splice_donor_variant | \n", "ENST00000546407.1:n.48_48+1delGG | \n", "splicing_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3474 | \n", "ENSG00000001626 | \n", "117105884 | \n", "AGGT | \n", "A | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | splicing_variant | \n", ". | \n", "splice_donor_variant | \n", "ENST00000546407.1:n.48_48+2delGGT | \n", "splicing_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3486 | \n", "ENSG00000001626 | \n", "117105885 | \n", "GG | \n", "G | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | splicing_variant | \n", ". | \n", "splice_donor_variant | \n", "ENST00000546407.1:n.48+1delG | \n", "splicing_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3487 | \n", "ENSG00000001626 | \n", "117105885 | \n", "GGT | \n", "G | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | splicing_variant | \n", ". | \n", "splice_donor_variant | \n", "ENST00000546407.1:n.48+1_48+2delGT | \n", "splicing_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
486 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3506 | \n", "ENSG00000001626 | \n", "117105887 | \n", "T | \n", "TA | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000546407 | \n", "n.48+3*>+A | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.48+2_48+3insA | \n", "intron_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3507 | \n", "ENSG00000001626 | \n", "117105887 | \n", "T | \n", "TAC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000546407 | \n", "n.48+3*>+AC | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.48+2_48+3insAC | \n", "intron_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3508 | \n", "ENSG00000001626 | \n", "117105887 | \n", "T | \n", "TATC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000546407 | \n", "n.48+3*>+ATC | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.48+2_48+3insATC | \n", "intron_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3509 | \n", "ENSG00000001626 | \n", "117105887 | \n", "T | \n", "TC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000546407 | \n", "n.48+3*>+C | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.48+2_48+3insC | \n", "intron_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3510 | \n", "ENSG00000001626 | \n", "117105887 | \n", "T | \n", "TCTA | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000546407 | \n", "n.48+3*>+CTA | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.48+2_48+3insCTA | \n", "intron_variant | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
66208 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
12941 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GA | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insA | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12942 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GAT | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insAT | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12943 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GC | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insC | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12944 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GCAT | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insCAT | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12945 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GCGA | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insCGA | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
8 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24393 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+A | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer27ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->A,ENST0000000308... | \n", "
24394 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GAG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+AG | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer8ENST00000426... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->AG,ENST000000030... | \n", "
24395 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GAT | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+AT | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer8ENST00000426... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->AT,ENST000000030... | \n", "
24396 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+C | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Trp19LeufsTer26ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->C,ENST0000000308... | \n", "
24399 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+G | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer27ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->G,ENST0000000308... | \n", "
1337 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20862 | \n", "ENSG00000001626 | \n", "117120148 | \n", "CATG | \n", "C | \n", ". | \n", "CODON_DELETION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>-ATG | \n", "inframe_variant | \n", ". | \n", "inframe_deletion | \n", "ENSP00000389119.1:p.Met1?ENST00000426809.1:c.1... | \n", "inframe_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000426809:wholegene,ENSG... | \n", "
24397 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GCGA | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+CGA | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18_Trp19insAspENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->CGA,ENST00000003... | \n", "
24398 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GCTA | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+CTA | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18_Trp19insTyrENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->CTA,ENST00000003... | \n", "
28750 | \n", "ENSG00000001626 | \n", "117149087 | \n", "G | \n", "GCGA | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg55X/c.165*>+CGA | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Arg55delinsSerGluENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon3:c.165-1->CGA,ENST0000000... | \n", "
28754 | \n", "ENSG00000001626 | \n", "117149087 | \n", "G | \n", "GTAC | \n", ". | \n", "CODON_CHANGE_PLUS_CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg55X/c.165*>+TAC | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Arg55delinsSerThrENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon3:c.165-1->TAC,ENST0000000... | \n", "
422 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136292 | \n", "ENSG00000001626 | \n", "117267828 | \n", "A | \n", "G | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Gly/c.544A>G | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183GlyENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136297 | \n", "ENSG00000001626 | \n", "117267829 | \n", "G | \n", "A | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Lys/c.545G>A | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183LysENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136298 | \n", "ENSG00000001626 | \n", "117267829 | \n", "G | \n", "C | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Thr/c.545G>C | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183ThrENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136307 | \n", "ENSG00000001626 | \n", "117267829 | \n", "G | \n", "T | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Ile/c.545G>T | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183IleENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136319 | \n", "ENSG00000001626 | \n", "117267830 | \n", "A | \n", "C | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Ser/c.546A>C | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183SerENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
273 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21380 | \n", "ENSG00000001626 | \n", "117120185 | \n", "TCCA | \n", "T | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X13*/c.38*>-CCA | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Ser13_Lys14delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon1:c.38_40d... | \n", "
24810 | \n", "ENSG00000001626 | \n", "117144335 | \n", "TACA | \n", "T | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X28*/c.83*>-ACA | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr28_Arg29delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.83_85d... | \n", "
24824 | \n", "ENSG00000001626 | \n", "117144336 | \n", "ACAG | \n", "A | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X28*/c.84*>-CAG | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr28_Arg29delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.84_86d... | \n", "
25230 | \n", "ENSG00000001626 | \n", "117144365 | \n", "TACC | \n", "T | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X38*/c.113*>-ACC | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr38_Gln39delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.113_11... | \n", "
25244 | \n", "ENSG00000001626 | \n", "117144366 | \n", "ACCA | \n", "A | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X38*/c.114*>-CCA | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr38_Gln39delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.114_11... | \n", "
145 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136269 | \n", "ENSG00000001626 | \n", "117267827 | \n", "G | \n", "A | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Val181Val/c.543G>A | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.545G>A(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136270 | \n", "ENSG00000001626 | \n", "117267827 | \n", "G | \n", "C | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Val181Val/c.543G>C | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.545G>C(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136279 | \n", "ENSG00000001626 | \n", "117267827 | \n", "G | \n", "T | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Val181Val/c.543G>T | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.545G>T(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136291 | \n", "ENSG00000001626 | \n", "117267828 | \n", "A | \n", "C | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Arg/c.544A>C | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.546A>C(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136320 | \n", "ENSG00000001626 | \n", "117267830 | \n", "A | \n", "G | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Arg/c.546A>G | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.548A>G(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
85 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
25976 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->A,ENST000000030... | \n", "
25977 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TATG | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->ATG,ENST0000000... | \n", "
25978 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TC | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->C,ENST000000030... | \n", "
25979 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TCGA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->CGA,ENST0000000... | \n", "
25980 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TG | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->G,ENST000000030... | \n", "
41993 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136604 | \n", "ENSG00000001626 | \n", "117267850 | \n", "GTTA | \n", "G | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X189Trpext*?/c.567*>-TTA | \n", "stop_lost | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.CysTer190TrpENST0000046879... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136618 | \n", "ENSG00000001626 | \n", "117267851 | \n", "TTAG | \n", "T | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>-TAG | \n", "stop_lost | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Ter191delextTer5ENST000004... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136619 | \n", "ENSG00000001626 | \n", "117267852 | \n", "T | \n", "A | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Lysext*?/c.568T>A | \n", "stop_lost | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Ter191LysextTer6ENST000004... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136620 | \n", "ENSG00000001626 | \n", "117267852 | \n", "T | \n", "C | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Glnext*?/c.568T>C | \n", "stop_lost | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Ter191GlnextTer6ENST000004... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
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10730 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TA | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insA | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10731 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TAG | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insAG | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10732 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TC | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insC | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10733 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TG | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insG | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10734 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TGC | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insGC | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
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20850 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+A | \n", "frameshift_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1_1insA | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
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1823 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20851 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CACT | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+ACT | \n", "inframe_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1_1insACT | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
20857 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CTGC | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+TGC | \n", "inframe_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1_1insTGC | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
20862 | \n", "ENSG00000001626 | \n", "117120148 | \n", "CATG | \n", "C | \n", ". | \n", "CODON_DELETION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>-ATG | \n", "inframe_variant | \n", ". | \n", "inframe_deletion | \n", "ENSP00000389119.1:p.Met1?ENST00000426809.1:c.1... | \n", "inframe_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000426809:wholegene,ENSG... | \n", "
24397 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GCGA | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+CGA | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18_Trp19insAspENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->CGA,ENST00000003... | \n", "
24398 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GCTA | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+CTA | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18_Trp19insTyrENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->CTA,ENST00000003... | \n", "
424 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136292 | \n", "ENSG00000001626 | \n", "117267828 | \n", "A | \n", "G | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Gly/c.544A>G | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183GlyENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136297 | \n", "ENSG00000001626 | \n", "117267829 | \n", "G | \n", "A | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Lys/c.545G>A | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183LysENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136298 | \n", "ENSG00000001626 | \n", "117267829 | \n", "G | \n", "C | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Thr/c.545G>C | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183ThrENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136307 | \n", "ENSG00000001626 | \n", "117267829 | \n", "G | \n", "T | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Ile/c.545G>T | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183IleENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136319 | \n", "ENSG00000001626 | \n", "117267830 | \n", "A | \n", "C | \n", ". | \n", "NON_SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Ser/c.546A>C | \n", "nonsynonymous_variant | \n", ". | \n", "missense_variant | \n", "ENSP00000419254.1:p.Arg183SerENST00000468795.1... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
277 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20939 | \n", "ENSG00000001626 | \n", "117120154 | \n", "G | \n", "GT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg3*/c.7*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Arg3TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.6_7ins... | \n", "
20940 | \n", "ENSG00000001626 | \n", "117120154 | \n", "G | \n", "GTA | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg3*/c.7*>+TA | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Arg3TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.6_7ins... | \n", "
21109 | \n", "ENSG00000001626 | \n", "117120166 | \n", "G | \n", "GT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Glu7*/c.19*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Glu7TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.18_19i... | \n", "
21148 | \n", "ENSG00000001626 | \n", "117120169 | \n", "A | \n", "AT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Lys8*/c.22*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Lys8TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.21_22i... | \n", "
21149 | \n", "ENSG00000001626 | \n", "117120169 | \n", "A | \n", "ATA | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Lys8*/c.22*>+TA | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Lys8TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.21_22i... | \n", "
797 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136269 | \n", "ENSG00000001626 | \n", "117267827 | \n", "G | \n", "A | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Val181Val/c.543G>A | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.545G>A(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136270 | \n", "ENSG00000001626 | \n", "117267827 | \n", "G | \n", "C | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Val181Val/c.543G>C | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.545G>C(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136279 | \n", "ENSG00000001626 | \n", "117267827 | \n", "G | \n", "T | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Val181Val/c.543G>T | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.545G>T(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136291 | \n", "ENSG00000001626 | \n", "117267828 | \n", "A | \n", "C | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Arg/c.544A>C | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.546A>C(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136320 | \n", "ENSG00000001626 | \n", "117267830 | \n", "A | \n", "G | \n", ". | \n", "SYNONYMOUS_CODING | \n", "CFTR | \n", "ENST00000468795 | \n", "p.Arg182Arg/c.546A>G | \n", "synonymous_variant | \n", ". | \n", "synonymous_variant | \n", "ENST00000468795.1:c.548A>G(p.%3D)ENST000004687... | \n", "synonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
88 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
25976 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->A,ENST000000030... | \n", "
25977 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TATG | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->ATG,ENST0000000... | \n", "
25978 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TC | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->C,ENST000000030... | \n", "
25979 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TCGA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->CGA,ENST0000000... | \n", "
25980 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TG | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->G,ENST000000030... | \n", "
42041 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136603 | \n", "ENSG00000001626 | \n", "117267850 | \n", "GTT | \n", "G | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X189X/c.567*>-TT | \n", "frameshift_variant | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Cys190TerENST00000468795.1... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136604 | \n", "ENSG00000001626 | \n", "117267850 | \n", "GTTA | \n", "G | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X189Trpext*?/c.567*>-TTA | \n", "stop_lost | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.CysTer190TrpENST0000046879... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136608 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TA | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+A | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191IlefsTer6ENST0000046... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136609 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TC | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+C | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191LeufsTer6ENST0000046... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136610 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TCT | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+CT | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191LeufsTer11ENST000004... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
98 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136632 | \n", "ENSG00000001626 | \n", "117267852 | \n", "TAGA | \n", "T | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.569*>-AGA | \n", "stop_lost | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*1_571delAGA | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136645 | \n", "ENSG00000001626 | \n", "117267853 | \n", "AGA | \n", "A | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X190X/c.570*>-GA | \n", "frameshift_variant | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*1_572delGA | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136646 | \n", "ENSG00000001626 | \n", "117267853 | \n", "AGAC | \n", "A | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.570*>-GAC | \n", "stop_lost | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*2_572delGAC | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136649 | \n", "ENSG00000001626 | \n", "117267854 | \n", "G | \n", "GA | \n", ". | \n", "UTR_3_PRIME | \n", "CFTR | \n", "ENST00000468795 | \n", "\n", " | 3_prime_UTR_variant | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*1_572insA | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136650 | \n", "ENSG00000001626 | \n", "117267854 | \n", "G | \n", "GACG | \n", ". | \n", "UTR_3_PRIME | \n", "CFTR | \n", "ENST00000468795 | \n", "\n", " | 3_prime_UTR_variant | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*1_572insACG | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
1036 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
259692 | \n", "ENSG00000232661 | \n", "117204728 | \n", "GAAC | \n", "G | \n", ". | \n", "UPSTREAM | \n", "AC000111.3 | \n", "ENST00000441019 | \n", "\n", " | upstream_gene_variant | \n", ". | \n", "non_coding_exon_variant | \n", "\n", " | ignored | \n", "ignored | \n", "ncRNA_exonic | \n", "NaN | \n", "
259705 | \n", "ENSG00000232661 | \n", "117204729 | \n", "AAC | \n", "A | \n", ". | \n", "UPSTREAM | \n", "AC000111.3 | \n", "ENST00000441019 | \n", "\n", " | upstream_gene_variant | \n", ". | \n", "non_coding_exon_variant | \n", "\n", " | ignored | \n", "ignored | \n", "ncRNA_exonic | \n", "NaN | \n", "
259706 | \n", "ENSG00000232661 | \n", "117204729 | \n", "AACT | \n", "A | \n", ". | \n", "UPSTREAM | \n", "AC000111.3 | \n", "ENST00000441019 | \n", "\n", " | upstream_gene_variant | \n", ". | \n", "non_coding_exon_variant | \n", "\n", " | ignored | \n", "ignored | \n", "ncRNA_exonic | \n", "NaN | \n", "
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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187474 | \n", "ENSG00000001626 | \n", "117355809 | \n", "C | \n", "CGT | \n", ". | \n", "SPLICE_SITE_ACCEPTOR | \n", "CFTR | \n", "ENST00000600166 | \n", "\n", " | splicing_variant | \n", ". | \n", "intron_variant | \n", "ENST00000610149.1:n.450-3_450-2insGT | \n", "intron_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20853 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+G | \n", "frameshift_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1_1insG | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
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20855 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CT | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+T | \n", "frameshift_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1_1insT | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
160354 | \n", "ENSG00000001626 | \n", "117307159 | \n", "T | \n", "TC | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420Xext*?/c.4258*>+C | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000403677.1:p.Ter1420LeufsTer74ENST00000... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000454343:exon26:c.4257_... | \n", "
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160357 | \n", "ENSG00000001626 | \n", "117307159 | \n", "T | \n", "TGA | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420Xext*?/c.4258*>+GA | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000403677.1:p.Ter1420AspfsTer8ENST000004... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000454343:exon26:c.4257_... | \n", "
160358 | \n", "ENSG00000001626 | \n", "117307159 | \n", "T | \n", "TT | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420Xext*?/c.4258*>+T | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000403677.1:p.Ter1420LeufsTer74ENST00000... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000454343:exon26:c.4257d... | \n", "
160359 | \n", "ENSG00000001626 | \n", "117307159 | \n", "T | \n", "TTC | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420Xext*?/c.4258*>+TC | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000403677.1:p.Ter1420SerfsTer8ENST000004... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000454343:exon26:c.4257_... | \n", "
776 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
150498 | \n", "ENSG00000001626 | \n", "117304914 | \n", "T | \n", "TCGA | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Val1349_Thr1350insGluENST0... | \n", "inframe_variant | \n", "inframe_variant | \n", "nonframeshift insertion | \n", "ENSG00000001626:ENST00000426809:exon24:c.4046_... | \n", "
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11314 | \n", "ENSG00000001626 | \n", "117119398 | \n", "AGGT | \n", "A | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | splicing_variant | \n", ". | \n", "splice_donor_variant | \n", "ENST00000446805.1:c.-424_-424+2delGGT | \n", "splicing_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
11317 | \n", "ENSG00000001626 | \n", "117119399 | \n", "G | \n", "GA | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | splicing_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-424_-424+1insA | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
11318 | \n", "ENSG00000001626 | \n", "117119399 | \n", "G | \n", "GAT | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | splicing_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-424_-424+1insAT | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
36 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20862 | \n", "ENSG00000001626 | \n", "117120148 | \n", "CATG | \n", "C | \n", ". | \n", "CODON_DELETION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>-ATG | \n", "inframe_variant | \n", ". | \n", "inframe_deletion | \n", "ENSP00000389119.1:p.Met1?ENST00000426809.1:c.1... | \n", "inframe_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000426809:wholegene,ENSG... | \n", "
20939 | \n", "ENSG00000001626 | \n", "117120154 | \n", "G | \n", "GT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg3*/c.7*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Arg3TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.6_7ins... | \n", "
20940 | \n", "ENSG00000001626 | \n", "117120154 | \n", "G | \n", "GTA | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg3*/c.7*>+TA | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Arg3TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.6_7ins... | \n", "
21109 | \n", "ENSG00000001626 | \n", "117120166 | \n", "G | \n", "GT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Glu7*/c.19*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Glu7TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.18_19i... | \n", "
21148 | \n", "ENSG00000001626 | \n", "117120169 | \n", "A | \n", "AT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Lys8*/c.22*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Lys8TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.21_22i... | \n", "
1393 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21380 | \n", "ENSG00000001626 | \n", "117120185 | \n", "TCCA | \n", "T | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X13*/c.38*>-CCA | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Ser13_Lys14delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon1:c.38_40d... | \n", "
21594 | \n", "ENSG00000001626 | \n", "117120201 | \n", "G | \n", "GACT | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18delinsArgLeuENST00000... | \n", "inframe_variant | \n", "inframe_variant | \n", "nonframeshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.53_54i... | \n", "
21597 | \n", "ENSG00000001626 | \n", "117120201 | \n", "G | \n", "GCAG | \n", ". | \n", "SPLICE_SITE_DONOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18dupENST00000426809.1:... | \n", "inframe_variant | \n", "inframe_variant | \n", "nonframeshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.53_54i... | \n", "
24810 | \n", "ENSG00000001626 | \n", "117144335 | \n", "TACA | \n", "T | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X28*/c.83*>-ACA | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr28_Arg29delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.83_85d... | \n", "
24824 | \n", "ENSG00000001626 | \n", "117144336 | \n", "ACAG | \n", "A | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X28*/c.84*>-CAG | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr28_Arg29delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.84_86d... | \n", "
175 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136647 | \n", "ENSG00000001626 | \n", "117267854 | \n", "G | \n", "A | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190*/c.570G>A | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000468795.1:c.572G>A(p.%3D)ENST000004687... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
160391 | \n", "ENSG00000001626 | \n", "117307162 | \n", "G | \n", "A | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420*/c.4260G>A | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000454343.1:c.4260G>A(p.%3D)ENST00000454... | \n", "nonsynonymous_variant | \n", "synonymous_variant | \n", "synonymous SNV | \n", "ENSG00000001626:ENST00000454343:exon26:c.G4260... | \n", "
188918 | \n", "ENSG00000001626 | \n", "117355912 | \n", "A | \n", "G | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000600166 | \n", "p.*156*/c.467A>G | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000600166.1:c.469A>G(p.%3D)ENST000006001... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
188932 | \n", "ENSG00000001626 | \n", "117355913 | \n", "A | \n", "G | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000600166 | \n", "p.*156*/c.468A>G | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000600166.1:c.470A>G(p.%3D)ENST000006001... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
4 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24430 | \n", "ENSG00000001626 | \n", "117144308 | \n", "TG | \n", "T | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X19X/c.56*>-G | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Trp19TerENST00000426809.1:... | \n", "frameshift_variant | \n", "stop_gained | \n", "stopgain SNV | \n", "ENSG00000001626:ENST00000003084:exon2:c.56delG... | \n", "
24444 | \n", "ENSG00000001626 | \n", "117144309 | \n", "GG | \n", "G | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X19X/c.57*>-G | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Trp19TerENST00000426809.1:... | \n", "frameshift_variant | \n", "stop_gained | \n", "stopgain SNV | \n", "ENSG00000001626:ENST00000003084:exon2:c.57delG... | \n", "
24626 | \n", "ENSG00000001626 | \n", "117144322 | \n", "TT | \n", "T | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X24X/c.70*>-T | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Leu24TerENST00000426809.1:... | \n", "frameshift_variant | \n", "stop_gained | \n", "stopgain SNV | \n", "ENSG00000001626:ENST00000003084:exon2:c.70delT... | \n", "
24640 | \n", "ENSG00000001626 | \n", "117144323 | \n", "TT | \n", "T | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X24X/c.71*>-T | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Leu24TerENST00000426809.1:... | \n", "frameshift_variant | \n", "stop_gained | \n", "stopgain SNV | \n", "ENSG00000001626:ENST00000003084:exon2:c.71delT... | \n", "
24822 | \n", "ENSG00000001626 | \n", "117144336 | \n", "AC | \n", "A | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X28X/c.84*>-C | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Tyr28TerENST00000426809.1:... | \n", "frameshift_variant | \n", "stop_gained | \n", "stopgain SNV | \n", "ENSG00000001626:ENST00000003084:exon2:c.84delC... | \n", "
214 rows
0 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
28718 | \n", "ENSG00000001626 | \n", "117149085 | \n", "C | \n", "CA | \n", ". | \n", "SPLICE_SITE_ACCEPTOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
28719 | \n", "ENSG00000001626 | \n", "117149085 | \n", "C | \n", "CAC | \n", ". | \n", "SPLICE_SITE_ACCEPTOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
28720 | \n", "ENSG00000001626 | \n", "117149085 | \n", "C | \n", "CATG | \n", ". | \n", "SPLICE_SITE_ACCEPTOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
28721 | \n", "ENSG00000001626 | \n", "117149085 | \n", "C | \n", "CC | \n", ". | \n", "SPLICE_SITE_ACCEPTOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
28722 | \n", "ENSG00000001626 | \n", "117149085 | \n", "C | \n", "CG | \n", ". | \n", "SPLICE_SITE_ACCEPTOR | \n", "CFTR | \n", "ENST00000454343 | \n", "\n", " | splicing_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
48 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136603 | \n", "ENSG00000001626 | \n", "117267850 | \n", "GTT | \n", "G | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X189X/c.567*>-TT | \n", "frameshift_variant | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Cys190TerENST00000468795.1... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136616 | \n", "ENSG00000001626 | \n", "117267851 | \n", "TT | \n", "T | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X190X/c.568*>-T | \n", "frameshift_variant | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Ter191ArgENST00000468795.1... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136617 | \n", "ENSG00000001626 | \n", "117267851 | \n", "TTA | \n", "T | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X190X/c.568*>-TA | \n", "frameshift_variant | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Ter191AspENST00000468795.1... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136622 | \n", "ENSG00000001626 | \n", "117267852 | \n", "T | \n", "TA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190X/c.569*>+A | \n", "frameshift_variant | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Ter191TerENST00000468795.1... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136626 | \n", "ENSG00000001626 | \n", "117267852 | \n", "T | \n", "TG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190X/c.569*>+G | \n", "frameshift_variant | \n", ". | \n", "stop_lost | \n", "ENSP00000419254.1:p.Ter191TerENST00000468795.1... | \n", "stop_lost | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
33 rows
\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136632 | \n", "ENSG00000001626 | \n", "117267852 | \n", "TAGA | \n", "T | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.569*>-AGA | \n", "stop_lost | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*1_571delAGA | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136645 | \n", "ENSG00000001626 | \n", "117267853 | \n", "AGA | \n", "A | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000468795 | \n", "p.X190X/c.570*>-GA | \n", "frameshift_variant | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*1_572delGA | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136646 | \n", "ENSG00000001626 | \n", "117267853 | \n", "AGAC | \n", "A | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.570*>-GAC | \n", "stop_lost | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000468795.1:c.*2_572delGAC | \n", "3_prime_UTR_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
160376 | \n", "ENSG00000001626 | \n", "117307160 | \n", "TAGA | \n", "T | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420Xext*?/c.4259*>-AGA | \n", "stop_lost | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000454343.1:c.*1_4259delAGA | \n", "3_prime_UTR_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000454343:exon26:c.4259_... | \n", "
160389 | \n", "ENSG00000001626 | \n", "117307161 | \n", "AGA | \n", "A | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X1420X/c.4260*>-GA | \n", "frameshift_variant | \n", ". | \n", "3_prime_UTR_variant | \n", "ENST00000454343.1:c.*1_4260delGA | \n", "3_prime_UTR_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000454343:exon26:c.4260_... | \n", "
35 rows
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20834 | \n", "ENSG00000001626 | \n", "117120146 | \n", "ACCA | \n", "A | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000426809 | \n", "p.X1X/c.1*>-CCA | \n", "frameshift_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "\n", " | 5_prime_UTR_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000426809:wholegene,ENSG... | \n", "
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24805 | \n", "ENSG00000001626 | \n", "117144335 | \n", "T | \n", "TG | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Tyr28*/c.83*>+G | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Tyr28TerENST00000426809.1:... | \n", "frameshift_variant | \n", "stop_gained | \n", "stopgain SNV | \n", "ENSG00000001626:ENST00000003084:exon2:c.82_83i... | \n", "
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160391 | \n", "ENSG00000001626 | \n", "117307162 | \n", "G | \n", "A | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420*/c.4260G>A | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000454343.1:c.4260G>A(p.%3D)ENST00000454... | \n", "nonsynonymous_variant | \n", "synonymous_variant | \n", "synonymous SNV | \n", "ENSG00000001626:ENST00000454343:exon26:c.G4260... | \n", "
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25984 | \n", "ENSG00000001626 | \n", "117144419 | \n", "TA | \n", "T | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
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25986 | \n", "ENSG00000001626 | \n", "117144419 | \n", "TATG | \n", "T | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
25987 | \n", "ENSG00000001626 | \n", "117144420 | \n", "A | \n", "AA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
25988 | \n", "ENSG00000001626 | \n", "117144420 | \n", "A | \n", "AC | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "intron_variant | \n", "intronic | \n", "NaN | \n", "
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10730 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TA | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insA | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10731 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TAG | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insAG | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10732 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TC | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insC | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10733 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TG | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insG | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
10734 | \n", "ENSG00000001626 | \n", "117119357 | \n", "T | \n", "TGC | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "intron_variant | \n", "ENST00000546407.1:n.166+3495_166+3496insGC | \n", "intron_variant | \n", "upstream_gene_variant | \n", "upstream | \n", "NaN | \n", "
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20847 | \n", "ENSG00000001626 | \n", "117120147 | \n", "CCA | \n", "C | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X1X/c.1*>-CA | \n", "frameshift_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "\n", " | 5_prime_UTR_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000426809:wholegene,ENSG... | \n", "
20848 | \n", "ENSG00000001626 | \n", "117120147 | \n", "CCAT | \n", "C | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000426809 | \n", "p.X1X/c.1*>-CAT | \n", "frameshift_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "\n", " | 5_prime_UTR_variant | \n", "frameshift_variant | \n", "frameshift deletion | \n", "ENSG00000001626:ENST00000426809:wholegene,ENSG... | \n", "
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20852 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+C | \n", "frameshift_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1dupC | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20851 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CACT | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+ACT | \n", "inframe_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1_1insACT | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
20857 | \n", "ENSG00000001626 | \n", "117120148 | \n", "C | \n", "CTGC | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Met1X/c.1*>+TGC | \n", "inframe_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000454343.1:c.-1_1insTGC | \n", "5_prime_UTR_variant | \n", "5_prime_UTR_variant | \n", "UTR5 | \n", "NaN | \n", "
21380 | \n", "ENSG00000001626 | \n", "117120185 | \n", "TCCA | \n", "T | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X13*/c.38*>-CCA | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Ser13_Lys14delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon1:c.38_40d... | \n", "
24810 | \n", "ENSG00000001626 | \n", "117144335 | \n", "TACA | \n", "T | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X28*/c.83*>-ACA | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr28_Arg29delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.83_85d... | \n", "
24824 | \n", "ENSG00000001626 | \n", "117144336 | \n", "ACAG | \n", "A | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.X28*/c.84*>-CAG | \n", "stop_gained | \n", ". | \n", "stop_gained | \n", "ENSP00000389119.1:p.Tyr28_Arg29delinsTerENST00... | \n", "stop_gained | \n", "inframe_variant | \n", "nonframeshift deletion | \n", "ENSG00000001626:ENST00000003084:exon2:c.84_86d... | \n", "
124 rows
0 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20939 | \n", "ENSG00000001626 | \n", "117120154 | \n", "G | \n", "GT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg3*/c.7*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Arg3TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.6_7ins... | \n", "
20940 | \n", "ENSG00000001626 | \n", "117120154 | \n", "G | \n", "GTA | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg3*/c.7*>+TA | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Arg3TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.6_7ins... | \n", "
21109 | \n", "ENSG00000001626 | \n", "117120166 | \n", "G | \n", "GT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Glu7*/c.19*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Glu7TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.18_19i... | \n", "
21148 | \n", "ENSG00000001626 | \n", "117120169 | \n", "A | \n", "AT | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Lys8*/c.22*>+T | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Lys8TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.21_22i... | \n", "
21149 | \n", "ENSG00000001626 | \n", "117120169 | \n", "A | \n", "ATA | \n", ". | \n", "STOP_GAINED | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Lys8*/c.22*>+TA | \n", "stop_gained | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Lys8TerENST00000426809.1:c... | \n", "frameshift_variant | \n", "frameshift_variant | \n", "frameshift insertion | \n", "ENSG00000001626:ENST00000003084:exon1:c.21_22i... | \n", "
1262 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136647 | \n", "ENSG00000001626 | \n", "117267854 | \n", "G | \n", "A | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190*/c.570G>A | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000468795.1:c.572G>A(p.%3D)ENST000004687... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
160391 | \n", "ENSG00000001626 | \n", "117307162 | \n", "G | \n", "A | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000454343 | \n", "p.*1420*/c.4260G>A | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000454343.1:c.4260G>A(p.%3D)ENST00000454... | \n", "nonsynonymous_variant | \n", "synonymous_variant | \n", "synonymous SNV | \n", "ENSG00000001626:ENST00000454343:exon26:c.G4260... | \n", "
188918 | \n", "ENSG00000001626 | \n", "117355912 | \n", "A | \n", "G | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000600166 | \n", "p.*156*/c.467A>G | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000600166.1:c.469A>G(p.%3D)ENST000006001... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
188932 | \n", "ENSG00000001626 | \n", "117355913 | \n", "A | \n", "G | \n", ". | \n", "SYNONYMOUS_STOP | \n", "CFTR | \n", "ENST00000600166 | \n", "p.*156*/c.468A>G | \n", "synonymous_variant | \n", ". | \n", "stop_retained_variant | \n", "ENST00000600166.1:c.470A>G(p.%3D)ENST000006001... | \n", "nonsynonymous_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
4 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
136608 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TA | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+A | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191IlefsTer6ENST0000046... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136609 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TC | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+C | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191LeufsTer6ENST0000046... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136610 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TCT | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+CT | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191LeufsTer11ENST000004... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136611 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TG | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+G | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191ValfsTer6ENST0000046... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
136612 | \n", "ENSG00000001626 | \n", "117267851 | \n", "T | \n", "TGA | \n", ". | \n", "STOP_LOST | \n", "CFTR | \n", "ENST00000468795 | \n", "p.*190Xext*?/c.568*>+GA | \n", "stop_lost | \n", ". | \n", "frameshift_variant | \n", "ENSP00000419254.1:p.Ter191AspfsTer11ENST000004... | \n", "frameshift_variant | \n", "ignored | \n", "unknown | \n", "UNKNOWN | \n", "
24 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
176140 | \n", "ENSG00000001626 | \n", "117350702 | \n", "TGAT | \n", "T | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000600166 | \n", "c.367-5109*>-GAT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000429014.1:n.210-5109_210-5107delGAT | \n", "intron_variant | \n", "3_prime_UTR_variant | \n", "UTR3 | \n", "NaN | \n", "
176153 | \n", "ENSG00000001626 | \n", "117350703 | \n", "GAT | \n", "G | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000600166 | \n", "c.367-5108*>-AT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000429014.1:n.210-5108_210-5107delAT | \n", "intron_variant | \n", "3_prime_UTR_variant | \n", "UTR3 | \n", "NaN | \n", "
176154 | \n", "ENSG00000001626 | \n", "117350703 | \n", "GATT | \n", "G | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000600166 | \n", "c.367-5108*>-ATT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000429014.1:n.210-5108_210-5106delATT | \n", "intron_variant | \n", "3_prime_UTR_variant | \n", "UTR3 | \n", "NaN | \n", "
176167 | \n", "ENSG00000001626 | \n", "117350704 | \n", "ATT | \n", "A | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000600166 | \n", "c.367-5107*>-TT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000429014.1:n.210-5107_210-5106delTT | \n", "intron_variant | \n", "3_prime_UTR_variant | \n", "UTR3 | \n", "NaN | \n", "
176168 | \n", "ENSG00000001626 | \n", "117350704 | \n", "ATTT | \n", "A | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000600166 | \n", "c.367-5107*>-TTT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000429014.1:n.210-5107_210-5105delTTT | \n", "intron_variant | \n", "3_prime_UTR_variant | \n", "UTR3 | \n", "NaN | \n", "
34 rows
0 rows
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
11346 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TA | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-424+3*>+A | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-424+2_-424+3insA | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
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11348 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-424+3*>+C | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-424+2_-424+3insC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
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11350 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TG | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-424+3*>+G | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-424+2_-424+3insG | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
11351 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TGCT | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-424+3*>+GCT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-424+2_-424+3insGCT | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
11352 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TGT | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-424+3*>+GT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-424+1_-424+2dupGT | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
11353 | \n", "ENSG00000001626 | \n", "117119401 | \n", "T | \n", "TT | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-424+3*>+T | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-424+2dupT | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12941 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GA | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insA | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12942 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GAT | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insAT | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12943 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GC | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insC | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12944 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GCAT | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insCAT | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12945 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GCGA | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insCGA | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12946 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GG | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1dupG | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12947 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GGA | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insGA | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
12948 | \n", "ENSG00000001626 | \n", "117119515 | \n", "G | \n", "GT | \n", ". | \n", "UTR_5_PRIME | \n", "CFTR | \n", "ENST00000446805 | \n", "\n", " | 5_prime_UTR_variant | \n", ". | \n", "5_prime_UTR_variant | \n", "ENST00000446805.1:c.-423-1_-423insT | \n", "5_prime_UTR_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16232 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TA | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+A | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2_-191+3insA | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16233 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+C | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2_-191+3insC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16234 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TCA | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+CA | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2_-191+3insCA | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16235 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TCTA | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+CTA | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2_-191+3insCTA | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16236 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TG | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+G | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2_-191+3insG | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16237 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TGC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+GC | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2_-191+3insGC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16238 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TT | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+T | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2dupT | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
16239 | \n", "ENSG00000001626 | \n", "117119750 | \n", "T | \n", "TTCG | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+3*>+TCG | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+2_-191+3insTCG | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "NaN | \n", "
21622 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TA | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+A | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455_-191+456insA | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->A,ENST0000000308... | \n", "
21623 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TAC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+AC | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455_-191+456insAC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->AC,ENST000000030... | \n", "
21624 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TAGC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+AGC | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455_-191+456insAGC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->AGC,ENST00000003... | \n", "
21625 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+C | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455_-191+456insC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->C,ENST0000000308... | \n", "
21626 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TG | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+G | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455_-191+456insG | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->G,ENST0000000308... | \n", "
21627 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TGC | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+GC | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455_-191+456insGC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->GC,ENST000000030... | \n", "
21628 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TGCT | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+GCT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455_-191+456insGCT | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->GCT,ENST00000003... | \n", "
21629 | \n", "ENSG00000001626 | \n", "117120203 | \n", "T | \n", "TT | \n", ". | \n", "INTRON | \n", "CFTR | \n", "ENST00000446805 | \n", "c.-191+456*>+T | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000446805.1:c.-191+455dupT | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon1:c.53+2->T,ENST0000000308... | \n", "
24393 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+A | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer27ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->A,ENST0000000308... | \n", "
24394 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GAG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+AG | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer8ENST00000426... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->AG,ENST000000030... | \n", "
24395 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GAT | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+AT | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer8ENST00000426... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->AT,ENST000000030... | \n", "
24396 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GC | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+C | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Trp19LeufsTer26ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->C,ENST0000000308... | \n", "
24397 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GCGA | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+CGA | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18_Trp19insAspENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->CGA,ENST00000003... | \n", "
24398 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GCTA | \n", ". | \n", "CODON_INSERTION | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+CTA | \n", "inframe_variant | \n", ". | \n", "inframe_insertion | \n", "ENSP00000389119.1:p.Ser18_Trp19insTyrENST00000... | \n", "inframe_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->CTA,ENST00000003... | \n", "
24399 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+G | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Ser18ArgfsTer27ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->G,ENST0000000308... | \n", "
24400 | \n", "ENSG00000001626 | \n", "117144306 | \n", "G | \n", "GT | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Ser18X/c.54*>+T | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Trp19LeufsTer26ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.54-1->T,ENST0000000308... | \n", "
25976 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->A,ENST000000030... | \n", "
25977 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TATG | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->ATG,ENST0000000... | \n", "
25978 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TC | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->C,ENST000000030... | \n", "
25979 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TCGA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->CGA,ENST0000000... | \n", "
25980 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TG | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->G,ENST000000030... | \n", "
25981 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TGC | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->GC,ENST00000003... | \n", "
25982 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TT | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->T,ENST000000030... | \n", "
25983 | \n", "ENSG00000001626 | \n", "117144419 | \n", "T | \n", "TTA | \n", ". | \n", "DOWNSTREAM | \n", "CFTR | \n", "ENST00000546407 | \n", "\n", " | downstream_gene_variant | \n", ". | \n", "downstream_gene_variant | \n", "\n", " | downstream_gene_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon2:c.164+2->TA,ENST00000003... | \n", "
28747 | \n", "ENSG00000001626 | \n", "117149087 | \n", "G | \n", "GA | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg55X/c.165*>+A | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Glu56ArgfsTer4ENST00000426... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon3:c.165-1->A,ENST000000030... | \n", "
28748 | \n", "ENSG00000001626 | \n", "117149087 | \n", "G | \n", "GAG | \n", ". | \n", "FRAME_SHIFT | \n", "CFTR | \n", "ENST00000454343 | \n", "p.Arg55X/c.165*>+AG | \n", "frameshift_variant | \n", ". | \n", "frameshift_variant | \n", "ENSP00000389119.1:p.Trp57AsnfsTer35ENST0000042... | \n", "frameshift_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon3:c.165-1->AG,ENST00000003... | \n", "
50 rows \u00d7 17 columns
\n", "\n", " | Gene | \n", "POS | \n", "REF | \n", "ALT | \n", "ID_x | \n", "Effect | \n", "Gene_Name | \n", "Transcript_ID | \n", "hgvs_snpeff | \n", "normalized_so_snpeff | \n", "ID_y | \n", "Consequence | \n", "hgvs_vep | \n", "normalized_so_vep | \n", "normalized_so_annovar | \n", "combined_effect | \n", "hgvs | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
249128 | \n", "ENSG00000083622 | \n", "117282491 | \n", "G | \n", "GG | \n", ". | \n", "INTRON | \n", "AC000111.6 | \n", "ENST00000456270 | \n", "n.65+4913*>+C | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000456270.1:n.65+4913dupC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon22:c.3535-1->G,ENST0000000... | \n", "
249129 | \n", "ENSG00000083622 | \n", "117282491 | \n", "G | \n", "GGA | \n", ". | \n", "INTRON | \n", "AC000111.6 | \n", "ENST00000456270 | \n", "n.65+4913*>+CT | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000456270.1:n.65+4913_65+4914insTC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon22:c.3535-1->GA,ENST000000... | \n", "
249131 | \n", "ENSG00000083622 | \n", "117282491 | \n", "G | \n", "GGT | \n", ". | \n", "INTRON | \n", "AC000111.6 | \n", "ENST00000456270 | \n", "n.65+4913*>+CA | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000456270.1:n.65+4912_65+4913dupAC | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon22:c.3535-1->GT,ENST000000... | \n", "
249132 | \n", "ENSG00000083622 | \n", "117282491 | \n", "G | \n", "GT | \n", ". | \n", "INTRON | \n", "AC000111.6 | \n", "ENST00000456270 | \n", "n.65+4913*>+A | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000456270.1:n.65+4913_65+4914insA | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon22:c.3535-1->T,ENST0000000... | \n", "
249133 | \n", "ENSG00000083622 | \n", "117282491 | \n", "G | \n", "T | \n", ". | \n", "INTRON | \n", "AC000111.6 | \n", "ENST00000456270 | \n", "n.65+4914C>A | \n", "intron_variant | \n", ". | \n", "intron_variant | \n", "ENST00000456270.1:n.65+4914C>A | \n", "intron_variant | \n", "splicing_variant | \n", "splicing | \n", "ENST00000454343:exon22:c.3535-1G>T,ENST0000000... | \n", "
5 rows \u00d7 17 columns
\n", "