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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: 3-120641660-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=120641660&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 120641660,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000187.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Arg",
"transcript": "NM_000187.4",
"protein_id": "NP_000178.2",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 445,
"cds_start": 808,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000283871.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000187.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Arg",
"transcript": "ENST00000283871.10",
"protein_id": "ENSP00000283871.5",
"transcript_support_level": 1,
"aa_start": 270,
"aa_end": null,
"aa_length": 445,
"cds_start": 808,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000187.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000283871.10"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.970G>A",
"hgvs_p": "p.Gly324Arg",
"transcript": "ENST00000898838.1",
"protein_id": "ENSP00000568897.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 499,
"cds_start": 970,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898838.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Arg",
"transcript": "ENST00000898833.1",
"protein_id": "ENSP00000568892.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 452,
"cds_start": 808,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898833.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.802G>A",
"hgvs_p": "p.Gly268Arg",
"transcript": "ENST00000898830.1",
"protein_id": "ENSP00000568889.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 443,
"cds_start": 802,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898830.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.796G>A",
"hgvs_p": "p.Gly266Arg",
"transcript": "ENST00000898840.1",
"protein_id": "ENSP00000568899.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 441,
"cds_start": 796,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898840.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.736G>A",
"hgvs_p": "p.Gly246Arg",
"transcript": "ENST00000898835.1",
"protein_id": "ENSP00000568894.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 421,
"cds_start": 736,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898835.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Gly244Arg",
"transcript": "ENST00000898841.1",
"protein_id": "ENSP00000568900.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 419,
"cds_start": 730,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898841.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Gly244Arg",
"transcript": "ENST00000955340.1",
"protein_id": "ENSP00000625399.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 419,
"cds_start": 730,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955340.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "ENST00000898842.1",
"protein_id": "ENSP00000568901.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 377,
"cds_start": 583,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898842.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "ENST00000898831.1",
"protein_id": "ENSP00000568890.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 370,
"cds_start": 583,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898831.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.577G>A",
"hgvs_p": "p.Gly193Arg",
"transcript": "ENST00000898834.1",
"protein_id": "ENSP00000568893.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 368,
"cds_start": 577,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898834.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.541G>A",
"hgvs_p": "p.Gly181Arg",
"transcript": "ENST00000898844.1",
"protein_id": "ENSP00000568903.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 356,
"cds_start": 541,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898844.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Arg",
"transcript": "ENST00000898832.1",
"protein_id": "ENSP00000568891.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 342,
"cds_start": 808,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898832.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.802G>A",
"hgvs_p": "p.Gly268Arg",
"transcript": "ENST00000898836.1",
"protein_id": "ENSP00000568895.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 340,
"cds_start": 802,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898836.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "ENST00000898837.1",
"protein_id": "ENSP00000568896.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 267,
"cds_start": 583,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898837.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Gly76Arg",
"transcript": "ENST00000494453.1",
"protein_id": "ENSP00000419163.1",
"transcript_support_level": 3,
"aa_start": 76,
"aa_end": null,
"aa_length": 144,
"cds_start": 226,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494453.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "XM_005247412.3",
"protein_id": "XP_005247469.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 370,
"cds_start": 583,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247412.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Arg",
"transcript": "XM_005247413.3",
"protein_id": "XP_005247470.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 338,
"cds_start": 808,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247413.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.385G>A",
"hgvs_p": "p.Gly129Arg",
"transcript": "XM_017006277.3",
"protein_id": "XP_016861766.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 304,
"cds_start": 385,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006277.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Arg",
"transcript": "XM_011512746.3",
"protein_id": "XP_011511048.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 294,
"cds_start": 808,
"cds_end": null,
"cds_length": 885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512746.3"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.583G>A",
"hgvs_p": "p.Gly195Arg",
"transcript": "XM_047448058.1",
"protein_id": "XP_047304014.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 263,
"cds_start": 583,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448058.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
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{
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],
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{
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{
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{
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],
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"gene_symbol": "HGD",
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"hgvs_c": "n.214G>A",
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"biotype": "nonsense_mediated_decay",
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],
"gene_symbol": "HGD",
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"dbsnp": "rs120074174",
"frequency_reference_population": 0.000031603096,
"hom_count_reference_population": 0,
"allele_count_reference_population": 51,
"gnomad_exomes_af": 0.0000294198,
"gnomad_genomes_af": 0.0000525742,
"gnomad_exomes_ac": 43,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.963390588760376,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.929,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9898,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.323,
"phylop100way_prediction": "Uncertain_significance",
"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": 15,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 15,
"benign_score": 0,
"pathogenic_score": 15,
"criteria": [
"PM1",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000187.4",
"gene_symbol": "HGD",
"hgnc_id": 4892,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Gly270Arg"
}
],
"clinvar_disease": "Alkaptonuria",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:1 O:1",
"phenotype_combined": "Alkaptonuria",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}