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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: 21-44531087-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=44531087&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 44531087,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_144991.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Arg197*",
"transcript": "NM_144991.3",
"protein_id": "NP_659428.2",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 669,
"cds_start": 589,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000323084.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144991.3"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Arg197*",
"transcript": "ENST00000323084.9",
"protein_id": "ENSP00000321987.4",
"transcript_support_level": 1,
"aa_start": 197,
"aa_end": null,
"aa_length": 669,
"cds_start": 589,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_144991.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000323084.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "n.544C>T",
"hgvs_p": null,
"transcript": "ENST00000397916.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000397916.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Arg197*",
"transcript": "ENST00000943283.1",
"protein_id": "ENSP00000613342.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 711,
"cds_start": 589,
"cds_end": null,
"cds_length": 2136,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943283.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "c.385C>T",
"hgvs_p": "p.Arg129*",
"transcript": "NM_001272037.2",
"protein_id": "NP_001258966.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 601,
"cds_start": 385,
"cds_end": null,
"cds_length": 1806,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001272037.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "n.*534C>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000642437.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287088",
"gene_hgnc_id": null,
"hgvs_c": "n.916G>A",
"hgvs_p": null,
"transcript": "ENST00000658407.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000658407.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124905038",
"gene_hgnc_id": null,
"hgvs_c": "n.3579G>A",
"hgvs_p": null,
"transcript": "XR_007067905.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007067905.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"hgvs_c": "n.*534C>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000642437.1"
}
],
"gene_symbol": "TSPEAR",
"gene_hgnc_id": 1268,
"dbsnp": "rs139455627",
"frequency_reference_population": 0.000565193,
"hom_count_reference_population": 1,
"allele_count_reference_population": 912,
"gnomad_exomes_af": 0.000597342,
"gnomad_genomes_af": 0.000256353,
"gnomad_exomes_ac": 873,
"gnomad_genomes_ac": 39,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.550000011920929,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.747,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_144991.3",
"gene_symbol": "TSPEAR",
"hgnc_id": 1268,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Arg197*"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000658407.1",
"gene_symbol": "ENSG00000287088",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.916G>A",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XR_007067905.1",
"gene_symbol": "LOC124905038",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3579G>A",
"hgvs_p": null
}
],
"clinvar_disease": " hair/tooth type with or without hypohidrosis,Ectodermal dysplasia 14,Inborn genetic diseases,TSPEAR-related disorder,TSPEAR-related disorder of tooth and hair follicle morphogenesis,not provided,not specified",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:1 US:1",
"phenotype_combined": "not specified|not provided|Ectodermal dysplasia 14, hair/tooth type with or without hypohidrosis|Inborn genetic diseases|TSPEAR-related disorder of tooth and hair follicle morphogenesis|TSPEAR-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}