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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: 10-68885620-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=68885620&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 68885620,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_152709.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.1824A>T",
"hgvs_p": "p.Glu608Asp",
"transcript": "NM_152709.5",
"protein_id": "NP_689922.3",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 989,
"cds_start": 1824,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000298596.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152709.5"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.1824A>T",
"hgvs_p": "p.Glu608Asp",
"transcript": "ENST00000298596.11",
"protein_id": "ENSP00000298596.6",
"transcript_support_level": 1,
"aa_start": 608,
"aa_end": null,
"aa_length": 989,
"cds_start": 1824,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152709.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298596.11"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.1824A>T",
"hgvs_p": "p.Glu608Asp",
"transcript": "ENST00000399169.8",
"protein_id": "ENSP00000382121.4",
"transcript_support_level": 1,
"aa_start": 608,
"aa_end": null,
"aa_length": 989,
"cds_start": 1824,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399169.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.663+1161A>T",
"hgvs_p": null,
"transcript": "ENST00000399165.8",
"protein_id": "ENSP00000382118.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": null,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399165.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.463+3510A>T",
"hgvs_p": null,
"transcript": "ENST00000399162.2",
"protein_id": "ENSP00000382115.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399162.2"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.2160A>T",
"hgvs_p": "p.Glu720Asp",
"transcript": "ENST00000642869.1",
"protein_id": "ENSP00000494558.1",
"transcript_support_level": null,
"aa_start": 720,
"aa_end": null,
"aa_length": 1101,
"cds_start": 2160,
"cds_end": null,
"cds_length": 3306,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000642869.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.1824A>T",
"hgvs_p": "p.Glu608Asp",
"transcript": "NM_001130161.4",
"protein_id": "NP_001123633.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 989,
"cds_start": 1824,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130161.4"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.1671A>T",
"hgvs_p": "p.Glu557Asp",
"transcript": "ENST00000909986.1",
"protein_id": "ENSP00000580045.1",
"transcript_support_level": null,
"aa_start": 557,
"aa_end": null,
"aa_length": 938,
"cds_start": 1671,
"cds_end": null,
"cds_length": 2817,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909986.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.1494A>T",
"hgvs_p": "p.Glu498Asp",
"transcript": "XM_011539454.3",
"protein_id": "XP_011537756.1",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 879,
"cds_start": 1494,
"cds_end": null,
"cds_length": 2640,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011539454.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.663+1161A>T",
"hgvs_p": null,
"transcript": "NM_001130159.3",
"protein_id": "NP_001123631.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": null,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130159.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"hgvs_c": "c.463+3510A>T",
"hgvs_p": null,
"transcript": "NM_001130160.3",
"protein_id": "NP_001123632.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130160.3"
}
],
"gene_symbol": "STOX1",
"gene_hgnc_id": 23508,
"dbsnp": "rs10509305",
"frequency_reference_population": 0.000003420258,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342026,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0265236496925354,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.155,
"revel_prediction": "Benign",
"alphamissense_score": 0.0615,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.561,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_152709.5",
"gene_symbol": "STOX1",
"hgnc_id": 23508,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1824A>T",
"hgvs_p": "p.Glu608Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}