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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: 4-122934228-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=122934228&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 122934228,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000274008.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "NM_145207.3",
"protein_id": "NP_660208.2",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 893,
"cds_start": 637,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 8116,
"mane_select": "ENST00000274008.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "ENST00000274008.5",
"protein_id": "ENSP00000274008.3",
"transcript_support_level": 1,
"aa_start": 213,
"aa_end": null,
"aa_length": 893,
"cds_start": 637,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 8116,
"mane_select": "NM_145207.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "n.679G>A",
"hgvs_p": null,
"transcript": "ENST00000422835.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 2492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "NM_001438322.1",
"protein_id": "NP_001425251.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 917,
"cds_start": 637,
"cds_end": null,
"cds_length": 2754,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 8188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "NM_001437913.1",
"protein_id": "NP_001424842.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 916,
"cds_start": 634,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 699,
"cdna_end": null,
"cdna_length": 8185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "ENST00000675612.1",
"protein_id": "ENSP00000502453.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 916,
"cds_start": 634,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 3414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "NM_001345856.2",
"protein_id": "NP_001332785.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 892,
"cds_start": 634,
"cds_end": null,
"cds_length": 2679,
"cdna_start": 699,
"cdna_end": null,
"cdna_length": 8113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "NM_001317799.2",
"protein_id": "NP_001304728.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 695,
"cds_start": 634,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 699,
"cdna_end": null,
"cdna_length": 2247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "XM_047449690.1",
"protein_id": "XP_047305646.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 835,
"cds_start": 637,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 2741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "XM_047449691.1",
"protein_id": "XP_047305647.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 834,
"cds_start": 634,
"cds_end": null,
"cds_length": 2505,
"cdna_start": 699,
"cdna_end": null,
"cdna_length": 2738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "XM_017007827.3",
"protein_id": "XP_016863316.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 823,
"cds_start": 637,
"cds_end": null,
"cds_length": 2472,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 9813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "XM_047449692.1",
"protein_id": "XP_047305648.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 814,
"cds_start": 637,
"cds_end": null,
"cds_length": 2445,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 2899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "XM_047449693.1",
"protein_id": "XP_047305649.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 799,
"cds_start": 637,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 9741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "XM_047449694.1",
"protein_id": "XP_047305650.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
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"cds_start": 634,
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"cdna_start": 699,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "XM_047449695.1",
"protein_id": "XP_047305651.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 796,
"cds_start": 637,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 5676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "XM_047449696.1",
"protein_id": "XP_047305652.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
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"cds_start": 634,
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"cdna_start": 699,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "XM_011531679.4",
"protein_id": "XP_011529981.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 790,
"cds_start": 637,
"cds_end": null,
"cds_length": 2373,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 2827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Asp212Asn",
"transcript": "XM_047449697.1",
"protein_id": "XP_047305653.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 789,
"cds_start": 634,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 699,
"cdna_end": null,
"cdna_length": 2824,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.181G>A",
"hgvs_p": "p.Asp61Asn",
"transcript": "XM_017007829.2",
"protein_id": "XP_016863318.1",
"transcript_support_level": null,
"aa_start": 61,
"aa_end": null,
"aa_length": 765,
"cds_start": 181,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn",
"transcript": "XM_017007830.2",
"protein_id": "XP_016863319.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 593,
"cds_start": 637,
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"cdna_start": 702,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "n.699G>A",
"hgvs_p": null,
"transcript": "ENST00000674886.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "n.211G>A",
"hgvs_p": null,
"transcript": "ENST00000675392.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1372,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "n.702G>A",
"hgvs_p": null,
"transcript": "XR_007096375.1",
"protein_id": null,
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{
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"protein_coding": false,
"strand": true,
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"non_coding_transcript_exon_variant"
],
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"exon_count": 13,
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"gene_symbol": "AFG2A",
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},
{
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"strand": true,
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"non_coding_transcript_exon_variant"
],
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"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2112,
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"feature": null
}
],
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"dbsnp": "rs139066705",
"frequency_reference_population": 0.00006505318,
"hom_count_reference_population": 1,
"allele_count_reference_population": 105,
"gnomad_exomes_af": 0.0000321503,
"gnomad_genomes_af": 0.000381128,
"gnomad_exomes_ac": 47,
"gnomad_genomes_ac": 58,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02996063232421875,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.126,
"revel_prediction": "Benign",
"alphamissense_score": 0.0696,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.483,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000274008.5",
"gene_symbol": "AFG2A",
"hgnc_id": 18119,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.637G>A",
"hgvs_p": "p.Asp213Asn"
}
],
"clinvar_disease": "Inborn genetic diseases,Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}