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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: 9-96251482-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=96251482&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 96251482,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000375263.8",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "c.389A>G",
"hgvs_p": "p.Asn130Ser",
"transcript": "NM_000197.2",
"protein_id": "NP_000188.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 310,
"cds_start": 389,
"cds_end": null,
"cds_length": 933,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 1159,
"mane_select": "ENST00000375263.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "c.389A>G",
"hgvs_p": "p.Asn130Ser",
"transcript": "ENST00000375263.8",
"protein_id": "ENSP00000364412.3",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 310,
"cds_start": 389,
"cds_end": null,
"cds_length": 933,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 1159,
"mane_select": "NM_000197.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "c.389A>G",
"hgvs_p": "p.Asn130Ser",
"transcript": "ENST00000375262.4",
"protein_id": "ENSP00000364411.2",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 260,
"cds_start": 389,
"cds_end": null,
"cds_length": 783,
"cdna_start": 389,
"cdna_end": null,
"cdna_length": 783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285269",
"gene_hgnc_id": null,
"hgvs_c": "n.*2065A>G",
"hgvs_p": null,
"transcript": "ENST00000643789.1",
"protein_id": "ENSP00000494818.1",
"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": 3333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285269",
"gene_hgnc_id": null,
"hgvs_c": "n.*2065A>G",
"hgvs_p": null,
"transcript": "ENST00000643789.1",
"protein_id": "ENSP00000494818.1",
"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": 3333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "c.281A>G",
"hgvs_p": "p.Asn94Ser",
"transcript": "ENST00000648799.1",
"protein_id": "ENSP00000498039.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 244,
"cds_start": 281,
"cds_end": null,
"cds_length": 737,
"cdna_start": 319,
"cdna_end": null,
"cdna_length": 775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "c.389A>G",
"hgvs_p": "p.Asn130Ser",
"transcript": "ENST00000650386.1",
"protein_id": "ENSP00000497464.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 157,
"cds_start": 389,
"cds_end": null,
"cds_length": 474,
"cdna_start": 407,
"cdna_end": null,
"cdna_length": 1404,
"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": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285269",
"gene_hgnc_id": null,
"hgvs_c": "n.1198A>G",
"hgvs_p": null,
"transcript": "ENST00000463517.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 2599,
"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": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285269",
"gene_hgnc_id": null,
"hgvs_c": "n.859A>G",
"hgvs_p": null,
"transcript": "ENST00000464104.6",
"protein_id": null,
"transcript_support_level": 5,
"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": 2000,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "n.*88A>G",
"hgvs_p": null,
"transcript": "ENST00000467499.6",
"protein_id": "ENSP00000498077.1",
"transcript_support_level": 3,
"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": 1079,
"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": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "n.389A>G",
"hgvs_p": null,
"transcript": "ENST00000648146.1",
"protein_id": "ENSP00000497238.1",
"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": 1068,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "n.389A>G",
"hgvs_p": null,
"transcript": "ENST00000650005.1",
"protein_id": "ENSP00000498121.1",
"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": 859,
"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": 20,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35D2-HSD17B3",
"gene_hgnc_id": null,
"hgvs_c": "n.3156A>G",
"hgvs_p": null,
"transcript": "NR_182427.1",
"protein_id": null,
"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": 3854,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "n.*88A>G",
"hgvs_p": null,
"transcript": "ENST00000467499.6",
"protein_id": "ENSP00000498077.1",
"transcript_support_level": 3,
"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": 1079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"hgvs_c": "n.202-6056A>G",
"hgvs_p": null,
"transcript": "ENST00000648332.1",
"protein_id": "ENSP00000497562.1",
"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": 607,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HSD17B3-AS1",
"gene_hgnc_id": 53136,
"hgvs_c": "n.244+4147T>C",
"hgvs_p": null,
"transcript": "ENST00000749286.1",
"protein_id": null,
"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": 476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HSD17B3",
"gene_hgnc_id": 5212,
"dbsnp": "rs119481079",
"frequency_reference_population": 0.00010904977,
"hom_count_reference_population": 0,
"allele_count_reference_population": 176,
"gnomad_exomes_af": 0.000116983,
"gnomad_genomes_af": 0.0000328528,
"gnomad_exomes_ac": 171,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9319220781326294,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.3700000047683716,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.873,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5458,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.311,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.37,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000375263.8",
"gene_symbol": "HSD17B3",
"hgnc_id": 5212,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.389A>G",
"hgvs_p": "p.Asn130Ser"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000643789.1",
"gene_symbol": "ENSG00000285269",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*2065A>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NR_182427.1",
"gene_symbol": "SLC35D2-HSD17B3",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3156A>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000749286.1",
"gene_symbol": "HSD17B3-AS1",
"hgnc_id": 53136,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.244+4147T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Testosterone 17-beta-dehydrogenase deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:2",
"phenotype_combined": "Testosterone 17-beta-dehydrogenase deficiency|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}