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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: 9-133704962-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=133704962&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 133704962,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000439388.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "NM_001134707.2",
"protein_id": "NP_001128179.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 918,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 1669,
"cdna_end": null,
"cdna_length": 3215,
"mane_select": "ENST00000439388.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "ENST00000439388.6",
"protein_id": "ENSP00000403084.1",
"transcript_support_level": 2,
"aa_start": 514,
"aa_end": null,
"aa_length": 918,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 1669,
"cdna_end": null,
"cdna_length": 3215,
"mane_select": "NM_001134707.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "ENST00000371872.8",
"protein_id": "ENSP00000360938.4",
"transcript_support_level": 1,
"aa_start": 514,
"aa_end": null,
"aa_length": 918,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 1798,
"cdna_end": null,
"cdna_length": 3344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "NM_007101.4",
"protein_id": "NP_009032.2",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 918,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 1833,
"cdna_end": null,
"cdna_length": 3379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "ENST00000427237.6",
"protein_id": "ENSP00000394210.2",
"transcript_support_level": 2,
"aa_start": 514,
"aa_end": null,
"aa_length": 607,
"cds_start": 1540,
"cds_end": null,
"cds_length": 1825,
"cdna_start": 1672,
"cdna_end": null,
"cdna_length": 1957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "XM_047422894.1",
"protein_id": "XP_047278850.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 918,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 1687,
"cdna_end": null,
"cdna_length": 3233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "XM_047422895.1",
"protein_id": "XP_047278851.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 918,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 1851,
"cdna_end": null,
"cdna_length": 3397,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "XM_017014367.2",
"protein_id": "XP_016869856.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 878,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 1833,
"cdna_end": null,
"cdna_length": 7032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "XM_047422896.1",
"protein_id": "XP_047278852.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 878,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 1669,
"cdna_end": null,
"cdna_length": 6868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*",
"transcript": "XM_047422897.1",
"protein_id": "XP_047278853.1",
"transcript_support_level": null,
"aa_start": 514,
"aa_end": null,
"aa_length": 878,
"cds_start": 1540,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 1687,
"cdna_end": null,
"cdna_length": 6886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "c.361C>T",
"hgvs_p": "p.Arg121*",
"transcript": "XM_047422898.1",
"protein_id": "XP_047278854.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 525,
"cds_start": 361,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 605,
"cdna_end": null,
"cdna_length": 2151,
"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": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "n.1833C>T",
"hgvs_p": null,
"transcript": "XR_001746213.2",
"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": 7395,
"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": 12,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "n.1833C>T",
"hgvs_p": null,
"transcript": "XR_001746216.2",
"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": 7254,
"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": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "n.1833C>T",
"hgvs_p": null,
"transcript": "XR_001746217.2",
"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": 6891,
"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": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"hgvs_c": "n.1833C>T",
"hgvs_p": null,
"transcript": "XR_007061258.1",
"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": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SARDH",
"gene_hgnc_id": 10536,
"dbsnp": "rs140559739",
"frequency_reference_population": 0.00009683741,
"hom_count_reference_population": 0,
"allele_count_reference_population": 153,
"gnomad_exomes_af": 0.000102257,
"gnomad_genomes_af": 0.0000459933,
"gnomad_exomes_ac": 146,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.25999999046325684,
"computational_prediction_selected": "Pathogenic",
"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": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.416,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000439388.6",
"gene_symbol": "SARDH",
"hgnc_id": 10536,
"effects": [
"stop_gained"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.1540C>T",
"hgvs_p": "p.Arg514*"
}
],
"clinvar_disease": "Sarcosine dehydrogenase deficiency",
"clinvar_classification": "Affects",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Sarcosine dehydrogenase deficiency",
"pathogenicity_classification_combined": "Affects",
"custom_annotations": null
}
],
"message": null
}