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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: 16-69321100-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=69321100&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 69321100,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_013245.3",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.901C>T",
"hgvs_p": "p.Gln301*",
"transcript": "NM_013245.3",
"protein_id": "NP_037377.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 437,
"cds_start": 901,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000254950.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013245.3"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.901C>T",
"hgvs_p": "p.Gln301*",
"transcript": "ENST00000254950.13",
"protein_id": "ENSP00000254950.11",
"transcript_support_level": 1,
"aa_start": 301,
"aa_end": null,
"aa_length": 437,
"cds_start": 901,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_013245.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000254950.13"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260914",
"gene_hgnc_id": null,
"hgvs_c": "c.973C>T",
"hgvs_p": "p.Gln325*",
"transcript": "ENST00000570054.3",
"protein_id": "ENSP00000461295.3",
"transcript_support_level": 5,
"aa_start": 325,
"aa_end": null,
"aa_length": 427,
"cds_start": 973,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000570054.3"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.898C>T",
"hgvs_p": "p.Gln300*",
"transcript": "ENST00000714474.1",
"protein_id": "ENSP00000519731.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 436,
"cds_start": 898,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714474.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.853C>T",
"hgvs_p": "p.Gln285*",
"transcript": "ENST00000907004.1",
"protein_id": "ENSP00000577063.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 421,
"cds_start": 853,
"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": "ENST00000907004.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.781C>T",
"hgvs_p": "p.Gln261*",
"transcript": "ENST00000949393.1",
"protein_id": "ENSP00000619452.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 397,
"cds_start": 781,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949393.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.778C>T",
"hgvs_p": "p.Gln260*",
"transcript": "ENST00000714473.1",
"protein_id": "ENSP00000519730.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 396,
"cds_start": 778,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714473.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.901C>T",
"hgvs_p": "p.Gln301*",
"transcript": "ENST00000949394.1",
"protein_id": "ENSP00000619453.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 390,
"cds_start": 901,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949394.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.901C>T",
"hgvs_p": "p.Gln301*",
"transcript": "ENST00000714476.1",
"protein_id": "ENSP00000519733.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 364,
"cds_start": 901,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714476.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Gln188*",
"transcript": "ENST00000714477.1",
"protein_id": "ENSP00000519734.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 324,
"cds_start": 562,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714477.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Gln188*",
"transcript": "ENST00000714480.1",
"protein_id": "ENSP00000519737.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 324,
"cds_start": 562,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714480.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Gln188*",
"transcript": "ENST00000714482.1",
"protein_id": "ENSP00000519739.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 324,
"cds_start": 562,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714482.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Gln188*",
"transcript": "ENST00000714483.1",
"protein_id": "ENSP00000519740.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 324,
"cds_start": 562,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000714483.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "c.863C>T",
"hgvs_p": "p.Pro288Leu",
"transcript": "ENST00000949392.1",
"protein_id": "ENSP00000619451.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 402,
"cds_start": 863,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949392.1"
},
{
"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": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.617C>T",
"hgvs_p": null,
"transcript": "ENST00000562754.1",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000562754.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.8C>T",
"hgvs_p": null,
"transcript": "ENST00000564399.1",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000564399.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*620C>T",
"hgvs_p": null,
"transcript": "ENST00000714472.1",
"protein_id": "ENSP00000519729.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714472.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.863C>T",
"hgvs_p": null,
"transcript": "ENST00000714475.1",
"protein_id": "ENSP00000519732.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714475.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*861C>T",
"hgvs_p": null,
"transcript": "ENST00000714478.1",
"protein_id": "ENSP00000519735.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714478.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.901C>T",
"hgvs_p": null,
"transcript": "ENST00000714479.1",
"protein_id": "ENSP00000519736.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714479.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*309C>T",
"hgvs_p": null,
"transcript": "ENST00000714481.1",
"protein_id": "ENSP00000519738.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714481.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*1044C>T",
"hgvs_p": null,
"transcript": "ENST00000714484.1",
"protein_id": "ENSP00000519741.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714484.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": 10,
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"exon_count": 12,
"intron_rank": null,
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"gene_symbol": "VPS4A",
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"cdna_start": null,
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"mane_select": null,
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714485.1"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
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"exon_count": 11,
"intron_rank": null,
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"gene_symbol": "VPS4A",
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"hgvs_c": "n.901C>T",
"hgvs_p": null,
"transcript": "ENST00000714486.1",
"protein_id": "ENSP00000519743.1",
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"cdna_start": null,
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"mane_select": null,
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714486.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*620C>T",
"hgvs_p": null,
"transcript": "ENST00000714472.1",
"protein_id": "ENSP00000519729.1",
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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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714472.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*861C>T",
"hgvs_p": null,
"transcript": "ENST00000714478.1",
"protein_id": "ENSP00000519735.1",
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"aa_end": null,
"aa_length": null,
"cds_start": null,
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"cdna_start": null,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714478.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*309C>T",
"hgvs_p": null,
"transcript": "ENST00000714481.1",
"protein_id": "ENSP00000519738.1",
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"aa_end": null,
"aa_length": null,
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"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714481.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.*1044C>T",
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"transcript": "ENST00000714484.1",
"protein_id": "ENSP00000519741.1",
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"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714484.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
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"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
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"transcript": "ENST00000714485.1",
"protein_id": "ENSP00000519742.1",
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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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000714485.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COG8",
"gene_hgnc_id": 18623,
"hgvs_c": "n.30-54G>A",
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"transcript": "ENST00000564419.1",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000564419.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"hgvs_c": "n.-111C>T",
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"transcript": "ENST00000566354.1",
"protein_id": null,
"transcript_support_level": 1,
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"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000566354.1"
}
],
"gene_symbol": "VPS4A",
"gene_hgnc_id": 13488,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5400000214576721,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.75,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_013245.3",
"gene_symbol": "VPS4A",
"hgnc_id": 13488,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.901C>T",
"hgvs_p": "p.Gln301*"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000570054.3",
"gene_symbol": "ENSG00000260914",
"hgnc_id": null,
"effects": [
"stop_gained"
],
"inheritance_mode": "",
"hgvs_c": "c.973C>T",
"hgvs_p": "p.Gln325*"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000564419.1",
"gene_symbol": "COG8",
"hgnc_id": 18623,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.30-54G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}