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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: 3-50294821-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=50294821&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 50294821,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003549.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "NM_003549.4",
"protein_id": "NP_003540.2",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 417,
"cds_start": 782,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000336307.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003549.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "ENST00000336307.6",
"protein_id": "ENSP00000337425.1",
"transcript_support_level": 1,
"aa_start": 261,
"aa_end": null,
"aa_length": 417,
"cds_start": 782,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003549.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336307.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "ENST00000450982.6",
"protein_id": "ENSP00000391922.1",
"transcript_support_level": 1,
"aa_start": 261,
"aa_end": null,
"aa_length": 387,
"cds_start": 782,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450982.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Arg12Gln",
"transcript": "ENST00000415204.5",
"protein_id": "ENSP00000401092.1",
"transcript_support_level": 1,
"aa_start": 12,
"aa_end": null,
"aa_length": 168,
"cds_start": 35,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415204.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Arg12Gln",
"transcript": "ENST00000513170.1",
"protein_id": "ENSP00000424633.1",
"transcript_support_level": 1,
"aa_start": 12,
"aa_end": null,
"aa_length": 138,
"cds_start": 35,
"cds_end": null,
"cds_length": 417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513170.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "NM_001200029.2",
"protein_id": "NP_001186958.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 417,
"cds_start": 782,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001200029.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "ENST00000621157.5",
"protein_id": "ENSP00000479935.1",
"transcript_support_level": 5,
"aa_start": 261,
"aa_end": null,
"aa_length": 417,
"cds_start": 782,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000621157.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "NM_001200030.2",
"protein_id": "NP_001186959.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 387,
"cds_start": 782,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001200030.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "ENST00000359051.7",
"protein_id": "ENSP00000351946.3",
"transcript_support_level": 5,
"aa_start": 261,
"aa_end": null,
"aa_length": 387,
"cds_start": 782,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359051.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "ENST00000919600.1",
"protein_id": "ENSP00000589659.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 387,
"cds_start": 782,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919600.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln",
"transcript": "ENST00000919601.1",
"protein_id": "ENSP00000589660.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 387,
"cds_start": 782,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000919601.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Arg12Gln",
"transcript": "NM_001200031.2",
"protein_id": "NP_001186960.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 168,
"cds_start": 35,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001200031.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Arg12Gln",
"transcript": "NM_001200032.2",
"protein_id": "NP_001186961.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 138,
"cds_start": 35,
"cds_end": null,
"cds_length": 417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001200032.2"
}
],
"gene_symbol": "HYAL3",
"gene_hgnc_id": 5322,
"dbsnp": "rs376527141",
"frequency_reference_population": 0.000030764277,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000174491,
"gnomad_genomes_af": 0.000150998,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 23,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0629153847694397,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.074,
"revel_prediction": "Benign",
"alphamissense_score": 0.0702,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.179,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_003549.4",
"gene_symbol": "HYAL3",
"hgnc_id": 5322,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.782G>A",
"hgvs_p": "p.Arg261Gln"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}