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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: 19-12899486-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12899486&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM5",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GCDH",
"hgnc_id": 4189,
"hgvs_c": "c.1262C>T",
"hgvs_p": "p.Ala421Val",
"inheritance_mode": "AR",
"pathogenic_score": 16,
"score": 16,
"transcript": "NM_000159.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SYCE2",
"hgnc_id": 27411,
"hgvs_c": "c.613-101G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_001105578.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM5,PP5_Very_Strong",
"acmg_score": 16,
"allele_count_reference_population": 195,
"alphamissense_prediction": null,
"alphamissense_score": 0.4768,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.57,
"chr": "19",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " type 1,Glutaric aciduria,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10 O:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.47883686423301697,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 438,
"aa_ref": "A",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1852,
"cdna_start": 1339,
"cds_end": null,
"cds_length": 1317,
"cds_start": 1262,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_000159.4",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1262C>T",
"hgvs_p": "p.Ala421Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000222214.10",
"protein_coding": true,
"protein_id": "NP_000150.1",
"strand": true,
"transcript": "NM_000159.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 438,
"aa_ref": "A",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1852,
"cdna_start": 1339,
"cds_end": null,
"cds_length": 1317,
"cds_start": 1262,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000222214.10",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1262C>T",
"hgvs_p": "p.Ala421Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000159.4",
"protein_coding": true,
"protein_id": "ENSP00000222214.4",
"strand": true,
"transcript": "ENST00000222214.10",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 438,
"aa_ref": "A",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1867,
"cdna_start": 1407,
"cds_end": null,
"cds_length": 1317,
"cds_start": 1262,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000591470.5",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1262C>T",
"hgvs_p": "p.Ala421Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466845.1",
"strand": true,
"transcript": "ENST00000591470.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 218,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1248,
"cdna_start": null,
"cds_end": null,
"cds_length": 657,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001105578.2",
"gene_hgnc_id": 27411,
"gene_symbol": "SYCE2",
"hgvs_c": "c.613-101G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000293695.8",
"protein_coding": true,
"protein_id": "NP_001099048.1",
"strand": false,
"transcript": "NM_001105578.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 218,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1248,
"cdna_start": null,
"cds_end": null,
"cds_length": 657,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000293695.8",
"gene_hgnc_id": 27411,
"gene_symbol": "SYCE2",
"hgvs_c": "c.613-101G>A",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001105578.2",
"protein_coding": true,
"protein_id": "ENSP00000293695.6",
"strand": false,
"transcript": "ENST00000293695.8",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 478,
"aa_ref": "A",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1918,
"cdna_start": 1435,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1382,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000940009.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1382C>T",
"hgvs_p": "p.Ala461Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610068.1",
"strand": true,
"transcript": "ENST00000940009.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 454,
"aa_ref": "A",
"aa_start": 437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1883,
"cdna_start": 1370,
"cds_end": null,
"cds_length": 1365,
"cds_start": 1310,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000587072.2",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1310C>T",
"hgvs_p": "p.Ala437Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468584.2",
"strand": true,
"transcript": "ENST00000587072.2",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 442,
"aa_ref": "A",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3022,
"cdna_start": 1340,
"cds_end": null,
"cds_length": 1329,
"cds_start": 1274,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000909380.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1274C>T",
"hgvs_p": "p.Ala425Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579439.1",
"strand": true,
"transcript": "ENST00000909380.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 438,
"aa_ref": "A",
"aa_start": 421,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3248,
"cdna_start": 1358,
"cds_end": null,
"cds_length": 1317,
"cds_start": 1262,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000909379.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1262C>T",
"hgvs_p": "p.Ala421Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579438.1",
"strand": true,
"transcript": "ENST00000909379.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 436,
"aa_ref": "A",
"aa_start": 419,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1795,
"cdna_start": 1313,
"cds_end": null,
"cds_length": 1311,
"cds_start": 1256,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000909381.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1256C>T",
"hgvs_p": "p.Ala419Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579440.1",
"strand": true,
"transcript": "ENST00000909381.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 436,
"aa_ref": "A",
"aa_start": 419,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1840,
"cdna_start": 1360,
"cds_end": null,
"cds_length": 1311,
"cds_start": 1256,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000909385.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1256C>T",
"hgvs_p": "p.Ala419Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579444.1",
"strand": true,
"transcript": "ENST00000909385.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 429,
"aa_ref": "A",
"aa_start": 412,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1771,
"cdna_start": 1290,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1235,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000714075.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1235C>T",
"hgvs_p": "p.Ala412Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519366.1",
"strand": true,
"transcript": "ENST00000714075.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 426,
"aa_ref": "A",
"aa_start": 409,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1786,
"cdna_start": 1303,
"cds_end": null,
"cds_length": 1281,
"cds_start": 1226,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000588905.6",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1226C>T",
"hgvs_p": "p.Ala409Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000465770.2",
"strand": true,
"transcript": "ENST00000588905.6",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 426,
"aa_ref": "A",
"aa_start": 409,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1830,
"cdna_start": 1348,
"cds_end": null,
"cds_length": 1281,
"cds_start": 1226,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000909383.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1226C>T",
"hgvs_p": "p.Ala409Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579442.1",
"strand": true,
"transcript": "ENST00000909383.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 426,
"aa_ref": "A",
"aa_start": 409,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1534,
"cdna_start": 1280,
"cds_end": null,
"cds_length": 1281,
"cds_start": 1226,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000909387.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1226C>T",
"hgvs_p": "p.Ala409Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579446.1",
"strand": true,
"transcript": "ENST00000909387.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 415,
"aa_ref": "A",
"aa_start": 398,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1751,
"cdna_start": 1270,
"cds_end": null,
"cds_length": 1248,
"cds_start": 1193,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000954317.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1193C>T",
"hgvs_p": "p.Ala398Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624376.1",
"strand": true,
"transcript": "ENST00000954317.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 405,
"aa_ref": "A",
"aa_start": 388,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2910,
"cdna_start": 1228,
"cds_end": null,
"cds_length": 1218,
"cds_start": 1163,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000954316.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1163C>T",
"hgvs_p": "p.Ala388Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624375.1",
"strand": true,
"transcript": "ENST00000954316.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 396,
"aa_ref": "A",
"aa_start": 379,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1414,
"cdna_start": 1202,
"cds_end": null,
"cds_length": 1191,
"cds_start": 1136,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000714072.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1136C>T",
"hgvs_p": "p.Ala379Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519363.1",
"strand": true,
"transcript": "ENST00000714072.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 396,
"aa_ref": "A",
"aa_start": 379,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1722,
"cdna_start": 1240,
"cds_end": null,
"cds_length": 1191,
"cds_start": 1136,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000909384.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1136C>T",
"hgvs_p": "p.Ala379Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579443.1",
"strand": true,
"transcript": "ENST00000909384.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 390,
"aa_ref": "A",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1667,
"cdna_start": 1184,
"cds_end": null,
"cds_length": 1173,
"cds_start": 1118,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000940008.1",
"gene_hgnc_id": 4189,
"gene_symbol": "GCDH",
"hgvs_c": "c.1118C>T",
"hgvs_p": "p.Ala373Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610067.1",
"strand": true,
"transcript": "ENST00000940008.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 383,
"aa_ref": "A",
"aa_start": 366,
"biotype": "protein_coding",
"canonical": false,
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]
}