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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: 14-74072539-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=74072539&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 74072539,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000553458.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Pro62Ser",
"transcript": "NM_005589.4",
"protein_id": "NP_005580.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 535,
"cds_start": 184,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 5462,
"mane_select": "ENST00000553458.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Pro62Ser",
"transcript": "ENST00000553458.6",
"protein_id": "ENSP00000450436.1",
"transcript_support_level": 1,
"aa_start": 62,
"aa_end": null,
"aa_length": 535,
"cds_start": 184,
"cds_end": null,
"cds_length": 1608,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 5462,
"mane_select": "NM_005589.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "n.282C>T",
"hgvs_p": null,
"transcript": "ENST00000554231.5",
"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": 1323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "n.239C>T",
"hgvs_p": null,
"transcript": "ENST00000554501.5",
"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": 2221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Pro62Ser",
"transcript": "NM_001278593.2",
"protein_id": "NP_001265522.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 522,
"cds_start": 184,
"cds_end": null,
"cds_length": 1569,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 5423,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Pro62Ser",
"transcript": "ENST00000350259.8",
"protein_id": "ENSP00000342564.4",
"transcript_support_level": 2,
"aa_start": 62,
"aa_end": null,
"aa_length": 522,
"cds_start": 184,
"cds_end": null,
"cds_length": 1569,
"cdna_start": 237,
"cdna_end": null,
"cdna_length": 1869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "c.-442C>T",
"hgvs_p": null,
"transcript": "NM_001278594.2",
"protein_id": "NP_001265523.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 381,
"cds_start": -4,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "n.237C>T",
"hgvs_p": null,
"transcript": "ENST00000556852.1",
"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": 726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "c.-442C>T",
"hgvs_p": null,
"transcript": "NM_001278594.2",
"protein_id": "NP_001265523.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 381,
"cds_start": -4,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "BBOF1",
"gene_hgnc_id": 19855,
"hgvs_c": "n.1380-5657G>A",
"hgvs_p": null,
"transcript": "ENST00000492026.4",
"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": 1715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"hgvs_c": "n.138-175C>T",
"hgvs_p": null,
"transcript": "ENST00000553814.5",
"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": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "BBOF1",
"gene_hgnc_id": 19855,
"hgvs_c": "n.1817-5657G>A",
"hgvs_p": null,
"transcript": "XR_007064048.1",
"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": 2050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "BBOF1",
"gene_hgnc_id": 19855,
"hgvs_c": "n.1709-5657G>A",
"hgvs_p": null,
"transcript": "XR_007064049.1",
"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": 1942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALDH6A1",
"gene_hgnc_id": 7179,
"dbsnp": "rs796065046",
"frequency_reference_population": 6.840497e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8405e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9925801753997803,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.800000011920929,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.988,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9168,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.365,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999476001251954,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000553458.6",
"gene_symbol": "ALDH6A1",
"hgnc_id": 7179,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Pro62Ser"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000492026.4",
"gene_symbol": "BBOF1",
"hgnc_id": 19855,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.1380-5657G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Methylmalonate semialdehyde dehydrogenase deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Methylmalonate semialdehyde dehydrogenase deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}