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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: 15-80173143-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=80173143&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 80173143,
"ref": "A",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000561421.6",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Gln279Arg",
"transcript": "NM_000137.4",
"protein_id": "NP_000128.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 419,
"cds_start": 836,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 892,
"cdna_end": null,
"cdna_length": 1456,
"mane_select": "ENST00000561421.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Gln279Arg",
"transcript": "ENST00000561421.6",
"protein_id": "ENSP00000453347.2",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 419,
"cds_start": 836,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 892,
"cdna_end": null,
"cdna_length": 1456,
"mane_select": "NM_000137.4",
"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": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "n.2864A>G",
"hgvs_p": null,
"transcript": "ENST00000539156.5",
"protein_id": null,
"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": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Gln279Arg",
"transcript": "NM_001374377.1",
"protein_id": "NP_001361306.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 419,
"cds_start": 836,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 982,
"cdna_end": null,
"cdna_length": 2146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Gln279Arg",
"transcript": "NM_001374380.1",
"protein_id": "NP_001361309.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 419,
"cds_start": 836,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 2082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Gln279Arg",
"transcript": "ENST00000261755.9",
"protein_id": "ENSP00000261755.5",
"transcript_support_level": 5,
"aa_start": 279,
"aa_end": null,
"aa_length": 419,
"cds_start": 836,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 1471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Gln279Arg",
"transcript": "ENST00000407106.5",
"protein_id": "ENSP00000385080.1",
"transcript_support_level": 5,
"aa_start": 279,
"aa_end": null,
"aa_length": 419,
"cds_start": 836,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 991,
"cdna_end": null,
"cdna_length": 2152,
"mane_select": null,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "n.764A>G",
"hgvs_p": null,
"transcript": "ENST00000558627.1",
"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": 842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "n.172A>G",
"hgvs_p": null,
"transcript": "ENST00000559542.1",
"protein_id": null,
"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": 782,
"mane_select": null,
"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": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "n.2450A>G",
"hgvs_p": null,
"transcript": "ENST00000646551.1",
"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": 3016,
"mane_select": null,
"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": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"hgvs_c": "n.925A>G",
"hgvs_p": null,
"transcript": "ENST00000682012.1",
"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": 1507,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FAH",
"gene_hgnc_id": 3579,
"dbsnp": "rs121965078",
"frequency_reference_population": 0.0000018586325,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.0000013681,
"gnomad_genomes_af": 0.00000657013,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9745622873306274,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9279999732971191,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.886,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4233,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.517,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.962283919338508,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000561421.6",
"gene_symbol": "FAH",
"hgnc_id": 3579,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.836A>G",
"hgvs_p": "p.Gln279Arg"
}
],
"clinvar_disease": "Tyrosinemia type I",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Tyrosinemia type I",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}