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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: 15-100905610-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=100905610&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 100905610,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000329841.10",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3",
"gene_hgnc_id": 409,
"hgvs_c": "c.1156A>G",
"hgvs_p": "p.Met386Val",
"transcript": "NM_000693.4",
"protein_id": "NP_000684.2",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 512,
"cds_start": 1156,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 3469,
"mane_select": "ENST00000329841.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3",
"gene_hgnc_id": 409,
"hgvs_c": "c.1156A>G",
"hgvs_p": "p.Met386Val",
"transcript": "ENST00000329841.10",
"protein_id": "ENSP00000332256.5",
"transcript_support_level": 1,
"aa_start": 386,
"aa_end": null,
"aa_length": 512,
"cds_start": 1156,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 3469,
"mane_select": "NM_000693.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3",
"gene_hgnc_id": 409,
"hgvs_c": "c.835A>G",
"hgvs_p": "p.Met279Val",
"transcript": "ENST00000346623.6",
"protein_id": "ENSP00000343294.6",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 405,
"cds_start": 835,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 3104,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3",
"gene_hgnc_id": 409,
"hgvs_c": "c.835A>G",
"hgvs_p": "p.Met279Val",
"transcript": "NM_001293815.2",
"protein_id": "NP_001280744.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 405,
"cds_start": 835,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 912,
"cdna_end": null,
"cdna_length": 3148,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3",
"gene_hgnc_id": 409,
"hgvs_c": "n.399A>G",
"hgvs_p": null,
"transcript": "ENST00000558869.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 586,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3-AS1",
"gene_hgnc_id": 55416,
"hgvs_c": "n.481-9544T>C",
"hgvs_p": null,
"transcript": "ENST00000560351.2",
"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": 3688,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3-AS1",
"gene_hgnc_id": 55416,
"hgvs_c": "n.589-9544T>C",
"hgvs_p": null,
"transcript": "ENST00000656756.1",
"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": 4312,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3-AS1",
"gene_hgnc_id": 55416,
"hgvs_c": "n.610-9544T>C",
"hgvs_p": null,
"transcript": "ENST00000659873.1",
"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": 1171,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3-AS1",
"gene_hgnc_id": 55416,
"hgvs_c": "n.329-9544T>C",
"hgvs_p": null,
"transcript": "ENST00000796528.1",
"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": 1714,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALDH1A3-AS1",
"gene_hgnc_id": 55416,
"hgvs_c": "n.481-9544T>C",
"hgvs_p": null,
"transcript": "NR_135827.1",
"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": 4204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALDH1A3",
"gene_hgnc_id": 409,
"dbsnp": "rs3803430",
"frequency_reference_population": 0.042302374,
"hom_count_reference_population": 4098,
"allele_count_reference_population": 68263,
"gnomad_exomes_af": 0.0357226,
"gnomad_genomes_af": 0.105481,
"gnomad_exomes_ac": 52208,
"gnomad_genomes_ac": 16055,
"gnomad_exomes_homalt": 2332,
"gnomad_genomes_homalt": 1766,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.002790480852127075,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.193,
"revel_prediction": "Benign",
"alphamissense_score": 0.0592,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.161,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000329841.10",
"gene_symbol": "ALDH1A3",
"hgnc_id": 409,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1156A>G",
"hgvs_p": "p.Met386Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000560351.2",
"gene_symbol": "ALDH1A3-AS1",
"hgnc_id": 55416,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.481-9544T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Isolated microphthalmia 8,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|Isolated microphthalmia 8|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}