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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: 5-233504-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=233504&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PP3_Strong",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SDHA",
"hgnc_id": 10680,
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"inheritance_mode": "AD,AR",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_004168.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Strong",
"PP5"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000286001",
"hgnc_id": null,
"hgvs_c": "n.923C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 11,
"score": 11,
"transcript": "ENST00000651543.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PP3_Strong,PP5",
"acmg_score": 11,
"allele_count_reference_population": 32,
"alphamissense_prediction": null,
"alphamissense_score": 0.9935,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.15,
"chr": "5",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " nuclear type 1,Gastrointestinal stromal tumor,Hereditary cancer-predisposing syndrome,Mitochondrial complex II deficiency,Pheochromocytoma/paraganglioma syndrome 5,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:3 US:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.971091628074646,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 664,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2693,
"cdna_start": 959,
"cds_end": null,
"cds_length": 1995,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_004168.4",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264932.11",
"protein_coding": true,
"protein_id": "NP_004159.2",
"strand": true,
"transcript": "NM_004168.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 664,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2693,
"cdna_start": 959,
"cds_end": null,
"cds_length": 1995,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000264932.11",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004168.4",
"protein_coding": true,
"protein_id": "ENSP00000264932.6",
"strand": true,
"transcript": "ENST00000264932.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 3665,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000651543.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000286001",
"hgvs_c": "n.923C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499215.1",
"strand": true,
"transcript": "ENST00000651543.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 726,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2511,
"cdna_start": 976,
"cds_end": null,
"cds_length": 2181,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000874235.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544294.1",
"strand": true,
"transcript": "ENST00000874235.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 715,
"aa_ref": "T",
"aa_start": 359,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2417,
"cdna_start": 1105,
"cds_end": null,
"cds_length": 2148,
"cds_start": 1076,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000952715.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Thr359Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622774.1",
"strand": true,
"transcript": "ENST00000952715.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 682,
"aa_ref": "T",
"aa_start": 326,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2355,
"cdna_start": 1021,
"cds_end": null,
"cds_length": 2049,
"cds_start": 977,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000874242.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.977C>T",
"hgvs_p": "p.Thr326Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544301.1",
"strand": true,
"transcript": "ENST00000874242.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 681,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2322,
"cdna_start": 959,
"cds_end": null,
"cds_length": 2046,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000952713.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622772.1",
"strand": true,
"transcript": "ENST00000952713.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 673,
"aa_ref": "T",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2306,
"cdna_start": 997,
"cds_end": null,
"cds_length": 2022,
"cds_start": 950,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000952712.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.950C>T",
"hgvs_p": "p.Thr317Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622771.1",
"strand": true,
"transcript": "ENST00000952712.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 672,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2285,
"cdna_start": 926,
"cds_end": null,
"cds_length": 2019,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000874248.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544307.1",
"strand": true,
"transcript": "ENST00000874248.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 666,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2333,
"cdna_start": 998,
"cds_end": null,
"cds_length": 2001,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000952708.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622767.1",
"strand": true,
"transcript": "ENST00000952708.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 663,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2324,
"cdna_start": 976,
"cds_end": null,
"cds_length": 1992,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000874234.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544293.1",
"strand": true,
"transcript": "ENST00000874234.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 663,
"aa_ref": "T",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2737,
"cdna_start": 1002,
"cds_end": null,
"cds_length": 1992,
"cds_start": 920,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000952707.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.920C>T",
"hgvs_p": "p.Thr307Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622766.1",
"strand": true,
"transcript": "ENST00000952707.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 656,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2260,
"cdna_start": 958,
"cds_end": null,
"cds_length": 1971,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000874246.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544305.1",
"strand": true,
"transcript": "ENST00000874246.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 653,
"aa_ref": "T",
"aa_start": 297,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2259,
"cdna_start": 925,
"cds_end": null,
"cds_length": 1962,
"cds_start": 890,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000874244.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.890C>T",
"hgvs_p": "p.Thr297Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544303.1",
"strand": true,
"transcript": "ENST00000874244.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 649,
"aa_ref": "T",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2215,
"cdna_start": 903,
"cds_end": null,
"cds_length": 1950,
"cds_start": 878,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000952716.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.878C>T",
"hgvs_p": "p.Thr293Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622775.1",
"strand": true,
"transcript": "ENST00000952716.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 626,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2194,
"cdna_start": 974,
"cds_end": null,
"cds_length": 1881,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000874236.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544295.1",
"strand": true,
"transcript": "ENST00000874236.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 616,
"aa_ref": "T",
"aa_start": 260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2549,
"cdna_start": 815,
"cds_end": null,
"cds_length": 1851,
"cds_start": 779,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001294332.2",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.779C>T",
"hgvs_p": "p.Thr260Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001281261.1",
"strand": true,
"transcript": "NM_001294332.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 616,
"aa_ref": "T",
"aa_start": 260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2148,
"cdna_start": 817,
"cds_end": null,
"cds_length": 1851,
"cds_start": 779,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000510361.5",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.779C>T",
"hgvs_p": "p.Thr260Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000427703.1",
"strand": true,
"transcript": "ENST00000510361.5",
"transcript_support_level": 2
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 609,
"aa_ref": "T",
"aa_start": 253,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2525,
"cdna_start": 794,
"cds_end": null,
"cds_length": 1830,
"cds_start": 758,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000874233.1",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.758C>T",
"hgvs_p": "p.Thr253Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544292.1",
"strand": true,
"transcript": "ENST00000874233.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 583,
"aa_ref": "T",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2450,
"cdna_start": 959,
"cds_end": null,
"cds_length": 1752,
"cds_start": 923,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001330758.2",
"gene_hgnc_id": 10680,
"gene_symbol": "SDHA",
"hgvs_c": "c.923C>T",
"hgvs_p": "p.Thr308Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317687.1",
"strand": true,
"transcript": "NM_001330758.2",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 583,
"aa_ref": "T",
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"feature": "XR_007058614.1",
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"gene_symbol": "SDHA",
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"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007058614.1",
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}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1457666982",
"effect": "missense_variant",
"frequency_reference_population": 0.000019826542,
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"gene_symbol": "SDHA",
"gnomad_exomes_ac": 31,
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"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Mitochondrial complex II deficiency, nuclear type 1;Pheochromocytoma/paraganglioma syndrome 5|Hereditary cancer-predisposing syndrome|Gastrointestinal stromal tumor|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.981,
"pos": 233504,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.578,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004168.4"
}
]
}