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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: 19-19258680-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=19258680&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 19258680,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_023002.3",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAPLN4",
"gene_hgnc_id": 31357,
"hgvs_c": "c.660A>G",
"hgvs_p": "p.Gln220Gln",
"transcript": "NM_023002.3",
"protein_id": "NP_075378.1",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 402,
"cds_start": 660,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000291481.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_023002.3"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAPLN4",
"gene_hgnc_id": 31357,
"hgvs_c": "c.660A>G",
"hgvs_p": "p.Gln220Gln",
"transcript": "ENST00000291481.8",
"protein_id": "ENSP00000291481.5",
"transcript_support_level": 1,
"aa_start": 220,
"aa_end": null,
"aa_length": 402,
"cds_start": 660,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_023002.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000291481.8"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAPLN4",
"gene_hgnc_id": 31357,
"hgvs_c": "c.732A>G",
"hgvs_p": "p.Gln244Gln",
"transcript": "ENST00000898464.1",
"protein_id": "ENSP00000568523.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 426,
"cds_start": 732,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898464.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAPLN4",
"gene_hgnc_id": 31357,
"hgvs_c": "c.558A>G",
"hgvs_p": "p.Gln186Gln",
"transcript": "ENST00000898466.1",
"protein_id": "ENSP00000568525.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 368,
"cds_start": 558,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898466.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAPLN4",
"gene_hgnc_id": 31357,
"hgvs_c": "c.474A>G",
"hgvs_p": "p.Gln158Gln",
"transcript": "ENST00000898465.1",
"protein_id": "ENSP00000568524.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 340,
"cds_start": 474,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898465.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267629",
"gene_hgnc_id": null,
"hgvs_c": "n.1791A>G",
"hgvs_p": null,
"transcript": "ENST00000586064.3",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000586064.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAPLN4",
"gene_hgnc_id": 31357,
"hgvs_c": "n.*166A>G",
"hgvs_p": null,
"transcript": "ENST00000592862.2",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000592862.2"
}
],
"gene_symbol": "HAPLN4",
"gene_hgnc_id": 31357,
"dbsnp": "rs80354663",
"frequency_reference_population": 0.001136382,
"hom_count_reference_population": 18,
"allele_count_reference_population": 1829,
"gnomad_exomes_af": 0.000618974,
"gnomad_genomes_af": 0.00608891,
"gnomad_exomes_ac": 902,
"gnomad_genomes_ac": 927,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 10,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5299999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.647,
"phylop100way_prediction": "Benign",
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_023002.3",
"gene_symbol": "HAPLN4",
"hgnc_id": 31357,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.660A>G",
"hgvs_p": "p.Gln220Gln"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000586064.3",
"gene_symbol": "ENSG00000267629",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1791A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}