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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: 21-44499878-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=44499878&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 44499878,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_144991.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "c.1915G>A",
"hgvs_p": "p.Asp639Asn",
"transcript": "NM_144991.3",
"protein_id": "NP_659428.2",
"transcript_support_level": null,
"aa_start": 639,
"aa_end": null,
"aa_length": 669,
"cds_start": 1915,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 1973,
"cdna_end": null,
"cdna_length": 3958,
"mane_select": "ENST00000323084.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "c.1915G>A",
"hgvs_p": "p.Asp639Asn",
"transcript": "ENST00000323084.9",
"protein_id": "ENSP00000321987.4",
"transcript_support_level": 1,
"aa_start": 639,
"aa_end": null,
"aa_length": 669,
"cds_start": 1915,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 1973,
"cdna_end": null,
"cdna_length": 3958,
"mane_select": "NM_144991.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "c.1711G>A",
"hgvs_p": "p.Asp571Asn",
"transcript": "NM_001272037.2",
"protein_id": "NP_001258966.1",
"transcript_support_level": null,
"aa_start": 571,
"aa_end": null,
"aa_length": 601,
"cds_start": 1711,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 2035,
"cdna_end": null,
"cdna_length": 4020,
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "n.*1860G>A",
"hgvs_p": null,
"transcript": "ENST00000642437.1",
"protein_id": "ENSP00000496535.1",
"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": 2790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "n.*1860G>A",
"hgvs_p": null,
"transcript": "ENST00000642437.1",
"protein_id": "ENSP00000496535.1",
"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": 2790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"dbsnp": "rs138480801",
"frequency_reference_population": 0.0037873413,
"hom_count_reference_population": 19,
"allele_count_reference_population": 6086,
"gnomad_exomes_af": 0.00394477,
"gnomad_genomes_af": 0.00228427,
"gnomad_exomes_ac": 5738,
"gnomad_genomes_ac": 348,
"gnomad_exomes_homalt": 18,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01287168264389038,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.276,
"revel_prediction": "Benign",
"alphamissense_score": 0.7693,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.096,
"phylop100way_prediction": "Uncertain_significance",
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_144991.3",
"gene_symbol": "TSPEAR",
"hgnc_id": 1268,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1915G>A",
"hgvs_p": "p.Asp639Asn"
}
],
"clinvar_disease": " 10, hair/tooth type with or without hypohidrosis, selective,Autosomal recessive nonsyndromic hearing loss 98,Ectodermal dysplasia 14,Inborn genetic diseases,TSPEAR-related disorder,Tooth agenesis,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:2 US:4 LB:2 B:2",
"phenotype_combined": "not specified|Ectodermal dysplasia 14, hair/tooth type with or without hypohidrosis|not provided|Inborn genetic diseases|Autosomal recessive nonsyndromic hearing loss 98|Tooth agenesis, selective, 10|TSPEAR-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}