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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: 8-43158710-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=43158710&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 43158710,
"ref": "A",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000379644.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp",
"transcript": "NM_152419.3",
"protein_id": "NP_689632.2",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 635,
"cds_start": 370,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 5227,
"mane_select": "ENST00000379644.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp",
"transcript": "ENST00000379644.9",
"protein_id": "ENSP00000368965.4",
"transcript_support_level": 2,
"aa_start": 124,
"aa_end": null,
"aa_length": 635,
"cds_start": 370,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 5227,
"mane_select": "NM_152419.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "n.220A>T",
"hgvs_p": null,
"transcript": "ENST00000520704.1",
"protein_id": "ENSP00000429109.1",
"transcript_support_level": 1,
"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": 1451,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.-464A>T",
"hgvs_p": null,
"transcript": "NM_001363229.2",
"protein_id": "NP_001350158.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 347,
"cds_start": -4,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp",
"transcript": "NM_001363227.2",
"protein_id": "NP_001350156.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 664,
"cds_start": 370,
"cds_end": null,
"cds_length": 1995,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 5314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp",
"transcript": "NM_001363228.2",
"protein_id": "NP_001350157.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 571,
"cds_start": 370,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 5035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.-464A>T",
"hgvs_p": null,
"transcript": "NM_001363229.2",
"protein_id": "NP_001350158.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 347,
"cds_start": -4,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp",
"transcript": "XM_005273409.2",
"protein_id": "XP_005273466.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 672,
"cds_start": 370,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 5338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp",
"transcript": "XM_005273411.2",
"protein_id": "XP_005273468.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 608,
"cds_start": 370,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 5146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp",
"transcript": "XM_005273412.5",
"protein_id": "XP_005273469.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 502,
"cds_start": 370,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 3010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "c.-464A>T",
"hgvs_p": null,
"transcript": "NM_001363229.2",
"protein_id": "NP_001350158.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 347,
"cds_start": -4,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"hgvs_c": "n.235-213A>T",
"hgvs_p": null,
"transcript": "ENST00000517319.1",
"protein_id": "ENSP00000430032.1",
"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": 491,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HGSNAT",
"gene_hgnc_id": 26527,
"dbsnp": "rs754875934",
"frequency_reference_population": 0.000018120152,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000186437,
"gnomad_genomes_af": 0.0000131392,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8664920926094055,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9359999895095825,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.646,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1123,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.021,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.3,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.990984146239472,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,PP5",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000379644.9",
"gene_symbol": "HGSNAT",
"hgnc_id": 26527,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.370A>T",
"hgvs_p": "p.Arg124Trp"
}
],
"clinvar_disease": " MPS-III-C,Mucopolysaccharidosis,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 73,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:3 LP:4 US:1",
"phenotype_combined": "Retinitis pigmentosa 73|Retinitis pigmentosa|Retinitis pigmentosa 73;Mucopolysaccharidosis, MPS-III-C|Mucopolysaccharidosis, MPS-III-C|Retinal dystrophy|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}