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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: 7-83961489-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=83961489&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SEMA3A",
"hgnc_id": 10723,
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"inheritance_mode": "AR,AD,SD",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_006080.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 48,
"alphamissense_prediction": null,
"alphamissense_score": 0.1753,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"chr": "7",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Hypogonadotropic hypogonadism 16 with or without anosmia,SEMA3A-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2 O:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1481187343597412,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8113,
"cdna_start": 2401,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_006080.3",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265362.9",
"protein_coding": true,
"protein_id": "NP_006071.1",
"strand": false,
"transcript": "NM_006080.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8113,
"cdna_start": 2401,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000265362.9",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006080.3",
"protein_coding": true,
"protein_id": "ENSP00000265362.3",
"strand": false,
"transcript": "ENST00000265362.9",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2550,
"cdna_start": 2362,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000436949.5",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000415260.1",
"strand": false,
"transcript": "ENST00000436949.5",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5944,
"cdna_start": 3066,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000864988.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535047.1",
"strand": false,
"transcript": "ENST00000864988.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3567,
"cdna_start": 2903,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000864989.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535048.1",
"strand": false,
"transcript": "ENST00000864989.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3232,
"cdna_start": 2568,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000864990.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535049.1",
"strand": false,
"transcript": "ENST00000864990.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3256,
"cdna_start": 2592,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000864991.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535050.1",
"strand": false,
"transcript": "ENST00000864991.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7241,
"cdna_start": 2668,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000864992.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535051.1",
"strand": false,
"transcript": "ENST00000864992.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3390,
"cdna_start": 2575,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000864994.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535053.1",
"strand": false,
"transcript": "ENST00000864994.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 731,
"aa_ref": "R",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3566,
"cdna_start": 2695,
"cds_end": null,
"cds_length": 2196,
"cds_start": 2078,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000864993.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Arg693His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535052.1",
"strand": false,
"transcript": "ENST00000864993.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 731,
"aa_ref": "R",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5725,
"cdna_start": 2581,
"cds_end": null,
"cds_length": 2196,
"cds_start": 2078,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000922179.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Arg693His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592238.1",
"strand": false,
"transcript": "ENST00000922179.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8421,
"cdna_start": 2709,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_005250110.4",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005250167.1",
"strand": false,
"transcript": "XM_005250110.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 771,
"aa_ref": "R",
"aa_start": 733,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8511,
"cdna_start": 2799,
"cds_end": null,
"cds_length": 2316,
"cds_start": 2198,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_047419751.1",
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Arg733His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275707.1",
"strand": false,
"transcript": "XM_047419751.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs318240753",
"effect": "missense_variant",
"frequency_reference_population": 0.000029742061,
"gene_hgnc_id": 10723,
"gene_symbol": "SEMA3A",
"gnomad_exomes_ac": 43,
"gnomad_exomes_af": 0.0000294159,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328766,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided|Hypogonadotropic hypogonadism 16 with or without anosmia|SEMA3A-related disorder",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.693,
"pos": 83961489,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.17,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006080.3"
}
]
}