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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: 17-3925408-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=3925408&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 3925408,
"ref": "T",
"alt": "C",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000397041.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.399A>G",
"hgvs_p": "p.Arg133Arg",
"transcript": "ENST00000572116.1",
"protein_id": "ENSP00000458865.1",
"transcript_support_level": 1,
"aa_start": 133,
"aa_end": null,
"aa_length": 142,
"cds_start": 399,
"cds_end": null,
"cds_length": 429,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 429,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*14A>G",
"hgvs_p": null,
"transcript": "NM_005173.4",
"protein_id": "NP_005164.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 999,
"cds_start": -4,
"cds_end": null,
"cds_length": 3000,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4695,
"mane_select": "ENST00000397041.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*14A>G",
"hgvs_p": null,
"transcript": "ENST00000397041.8",
"protein_id": "ENSP00000380234.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 999,
"cds_start": -4,
"cds_end": null,
"cds_length": 3000,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4695,
"mane_select": "NM_005173.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*14A>G",
"hgvs_p": null,
"transcript": "ENST00000397043.7",
"protein_id": "ENSP00000380236.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 998,
"cds_start": -4,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3197,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "ENST00000570845.5",
"protein_id": "ENSP00000461480.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 153,
"cds_start": -4,
"cds_end": null,
"cds_length": 462,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.3102A>G",
"hgvs_p": "p.Arg1034Arg",
"transcript": "NM_174955.3",
"protein_id": "NP_777615.1",
"transcript_support_level": null,
"aa_start": 1034,
"aa_end": null,
"aa_length": 1043,
"cds_start": 3102,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 3248,
"cdna_end": null,
"cdna_length": 4783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.3102A>G",
"hgvs_p": "p.Arg1034Arg",
"transcript": "ENST00000352011.7",
"protein_id": "ENSP00000301387.6",
"transcript_support_level": 5,
"aa_start": 1034,
"aa_end": null,
"aa_length": 1043,
"cds_start": 3102,
"cds_end": null,
"cds_length": 3132,
"cdna_start": 3157,
"cdna_end": null,
"cdna_length": 3274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.3099A>G",
"hgvs_p": "p.Arg1033Arg",
"transcript": "XM_011523885.2",
"protein_id": "XP_011522187.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1042,
"cds_start": 3099,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 3245,
"cdna_end": null,
"cdna_length": 4780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.3102A>G",
"hgvs_p": "p.Arg1034Arg",
"transcript": "XM_047436150.1",
"protein_id": "XP_047292106.1",
"transcript_support_level": null,
"aa_start": 1034,
"aa_end": null,
"aa_length": 1042,
"cds_start": 3102,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 3248,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.3099A>G",
"hgvs_p": "p.Arg1033Arg",
"transcript": "XM_047436151.1",
"protein_id": "XP_047292107.1",
"transcript_support_level": null,
"aa_start": 1033,
"aa_end": null,
"aa_length": 1041,
"cds_start": 3099,
"cds_end": null,
"cds_length": 3126,
"cdna_start": 3245,
"cdna_end": null,
"cdna_length": 4186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "n.841A>G",
"hgvs_p": null,
"transcript": "ENST00000570773.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "n.415A>G",
"hgvs_p": null,
"transcript": "ENST00000574999.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 776,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*14A>G",
"hgvs_p": null,
"transcript": "NM_174953.3",
"protein_id": "NP_777613.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1052,
"cds_start": -4,
"cds_end": null,
"cds_length": 3159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*14A>G",
"hgvs_p": null,
"transcript": "ENST00000359983.7",
"protein_id": "ENSP00000353072.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1052,
"cds_start": -4,
"cds_end": null,
"cds_length": 3159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "NM_174954.3",
"protein_id": "NP_777614.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1044,
"cds_start": -4,
"cds_end": null,
"cds_length": 3135,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "NM_174956.3",
"protein_id": "NP_777616.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1029,
"cds_start": -4,
"cds_end": null,
"cds_length": 3090,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "NM_174958.3",
"protein_id": "NP_777618.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1029,
"cds_start": -4,
"cds_end": null,
"cds_length": 3090,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4202,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "ENST00000309890.11",
"protein_id": "ENSP00000312577.7",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1029,
"cds_start": -4,
"cds_end": null,
"cds_length": 3090,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "ENST00000397035.8",
"protein_id": "ENSP00000380229.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1029,
"cds_start": -4,
"cds_end": null,
"cds_length": 3090,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*14A>G",
"hgvs_p": null,
"transcript": "NM_174957.3",
"protein_id": "NP_777617.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 998,
"cds_start": -4,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "XM_011523888.3",
"protein_id": "XP_011522190.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1028,
"cds_start": -4,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*25A>G",
"hgvs_p": null,
"transcript": "XM_047436152.1",
"protein_id": "XP_047292108.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1028,
"cds_start": -4,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4199,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"hgvs_c": "c.*14A>G",
"hgvs_p": null,
"transcript": "XM_047436153.1",
"protein_id": "XP_047292109.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 998,
"cds_start": -4,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 22,
"intron_rank": null,
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"gene_symbol": "ATP2A3",
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"hgvs_c": "c.*884A>G",
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"transcript": "XM_011523881.3",
"protein_id": "XP_011522183.1",
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"aa_start": null,
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"aa_length": 1114,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 4367,
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"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP2A3",
"gene_hgnc_id": 813,
"dbsnp": "rs887387",
"frequency_reference_population": 0.35662898,
"hom_count_reference_population": 104242,
"allele_count_reference_population": 575321,
"gnomad_exomes_af": 0.360163,
"gnomad_genomes_af": 0.322626,
"gnomad_exomes_ac": 526316,
"gnomad_genomes_ac": 49005,
"gnomad_exomes_homalt": 95894,
"gnomad_genomes_homalt": 8348,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.463,
"phylop100way_prediction": "Benign",
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000397041.8",
"gene_symbol": "ATP2A3",
"hgnc_id": 813,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*14A>G",
"hgvs_p": null
}
],
"clinvar_disease": "ATP2A3-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "ATP2A3-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}