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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 2-218344821-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218344821&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 218344821,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_015488.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.998T>G",
"hgvs_p": "p.Leu333Arg",
"transcript": "NM_015488.5",
"protein_id": "NP_056303.3",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 385,
"cds_start": 998,
"cds_end": null,
"cds_length": 1158,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": "ENST00000273077.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015488.5"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.998T>G",
"hgvs_p": "p.Leu333Arg",
"transcript": "ENST00000273077.9",
"protein_id": "ENSP00000273077.4",
"transcript_support_level": 1,
"aa_start": 333,
"aa_end": null,
"aa_length": 385,
"cds_start": 998,
"cds_end": null,
"cds_length": 1158,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": "NM_015488.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000273077.9"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.926T>G",
"hgvs_p": "p.Leu309Arg",
"transcript": "ENST00000258362.7",
"protein_id": "ENSP00000258362.3",
"transcript_support_level": 1,
"aa_start": 309,
"aa_end": null,
"aa_length": 361,
"cds_start": 926,
"cds_end": null,
"cds_length": 1086,
"cdna_start": 1021,
"cdna_end": null,
"cdna_length": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258362.7"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.1115T>G",
"hgvs_p": "p.Leu372Arg",
"transcript": "ENST00000685415.1",
"protein_id": "ENSP00000510415.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 424,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1275,
"cdna_start": 1137,
"cdna_end": null,
"cdna_length": 3100,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000685415.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.1097T>G",
"hgvs_p": "p.Leu366Arg",
"transcript": "ENST00000901530.1",
"protein_id": "ENSP00000571589.1",
"transcript_support_level": null,
"aa_start": 366,
"aa_end": null,
"aa_length": 418,
"cds_start": 1097,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 1114,
"cdna_end": null,
"cdna_length": 3086,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000901530.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.1028T>G",
"hgvs_p": "p.Leu343Arg",
"transcript": "ENST00000955416.1",
"protein_id": "ENSP00000625475.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 395,
"cds_start": 1028,
"cds_end": null,
"cds_length": 1188,
"cdna_start": 1055,
"cdna_end": null,
"cdna_length": 3011,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955416.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.989T>G",
"hgvs_p": "p.Leu330Arg",
"transcript": "ENST00000436005.3",
"protein_id": "ENSP00000414400.3",
"transcript_support_level": 5,
"aa_start": 330,
"aa_end": null,
"aa_length": 382,
"cds_start": 989,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 1011,
"cdna_end": null,
"cdna_length": 2974,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000436005.3"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.962T>G",
"hgvs_p": "p.Leu321Arg",
"transcript": "ENST00000689816.1",
"protein_id": "ENSP00000508450.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 373,
"cds_start": 962,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 984,
"cdna_end": null,
"cdna_length": 2919,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000689816.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.926T>G",
"hgvs_p": "p.Leu309Arg",
"transcript": "NM_022572.4",
"protein_id": "NP_072094.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 361,
"cds_start": 926,
"cds_end": null,
"cds_length": 1086,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022572.4"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Leu304Arg",
"transcript": "ENST00000901529.1",
"protein_id": "ENSP00000571588.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 356,
"cds_start": 911,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 933,
"cdna_end": null,
"cdna_length": 2903,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000901529.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.875T>G",
"hgvs_p": "p.Leu292Arg",
"transcript": "ENST00000688179.1",
"protein_id": "ENSP00000508635.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 344,
"cds_start": 875,
"cds_end": null,
"cds_length": 1035,
"cdna_start": 897,
"cdna_end": null,
"cdna_length": 2832,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000688179.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.818T>G",
"hgvs_p": "p.Leu273Arg",
"transcript": "ENST00000687736.1",
"protein_id": "ENSP00000509627.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 325,
"cds_start": 818,
"cds_end": null,
"cds_length": 978,
"cdna_start": 818,
"cdna_end": null,
"cdna_length": 2753,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000687736.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.638T>G",
"hgvs_p": "p.Leu213Arg",
"transcript": "ENST00000692295.1",
"protein_id": "ENSP00000509392.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 265,
"cds_start": 638,
"cds_end": null,
"cds_length": 798,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 2601,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000692295.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.617T>G",
"hgvs_p": "p.Leu206Arg",
"transcript": "ENST00000691220.1",
"protein_id": "ENSP00000509580.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 258,
"cds_start": 617,
"cds_end": null,
"cds_length": 777,
"cdna_start": 617,
"cdna_end": null,
"cdna_length": 2580,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000691220.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Leu304Arg",
"transcript": "XM_017003771.2",
"protein_id": "XP_016859260.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 356,
"cds_start": 911,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 2900,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003771.2"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "c.839T>G",
"hgvs_p": "p.Leu280Arg",
"transcript": "XM_017003772.2",
"protein_id": "XP_016859261.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 332,
"cds_start": 839,
"cds_end": null,
"cds_length": 999,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 2900,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003772.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.1756T>G",
"hgvs_p": null,
"transcript": "ENST00000684905.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3719,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000684905.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.1662T>G",
"hgvs_p": null,
"transcript": "ENST00000689098.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3625,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000689098.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.1795T>G",
"hgvs_p": null,
"transcript": "ENST00000689693.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3758,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000689693.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.*906T>G",
"hgvs_p": null,
"transcript": "ENST00000690891.1",
"protein_id": "ENSP00000509744.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3106,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000690891.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.253T>G",
"hgvs_p": null,
"transcript": "ENST00000691799.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2203,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000691799.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"hgvs_c": "n.*123T>G",
"hgvs_p": null,
"transcript": "ENST00000693423.1",
"protein_id": "ENSP00000508705.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2308,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000693423.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
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"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
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"hgvs_c": "n.320T>G",
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"transcript": "ENST00000693556.1",
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"cdna_start": null,
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"cdna_length": 2255,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000693556.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
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"hgvs_c": "n.*906T>G",
"hgvs_p": null,
"transcript": "ENST00000690891.1",
"protein_id": "ENSP00000509744.1",
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"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 3106,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000690891.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKD",
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"hgvs_c": "n.*123T>G",
"hgvs_p": null,
"transcript": "ENST00000693423.1",
"protein_id": "ENSP00000508705.1",
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"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2308,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000693423.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CATIP-AS2",
"gene_hgnc_id": 41079,
"hgvs_c": "n.146+6339A>C",
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"transcript": "ENST00000411433.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1203,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000411433.2"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
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"gene_symbol": "CATIP-AS2",
"gene_hgnc_id": 41079,
"hgvs_c": "n.120+6339A>C",
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"transcript": "NR_125777.1",
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"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1183,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_125777.1"
}
],
"gene_symbol": "PNKD",
"gene_hgnc_id": 9153,
"dbsnp": "rs1005386085",
"frequency_reference_population": 0.000008675606,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000821016,
"gnomad_genomes_af": 0.0000131479,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9013999700546265,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.921,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9412,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.884,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_015488.5",
"gene_symbol": "PNKD",
"hgnc_id": 9153,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.998T>G",
"hgvs_p": "p.Leu333Arg"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000411433.2",
"gene_symbol": "CATIP-AS2",
"hgnc_id": 41079,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.146+6339A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Paroxysmal nonkinesigenic dyskinesia",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Paroxysmal nonkinesigenic dyskinesia",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}