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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: 15-80979258-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=80979258&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 80979258,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_015154.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "c.666G>A",
"hgvs_p": "p.Lys222Lys",
"transcript": "NM_015154.3",
"protein_id": "NP_055969.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 234,
"cds_start": 666,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261758.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015154.3"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "c.666G>A",
"hgvs_p": "p.Lys222Lys",
"transcript": "ENST00000261758.6",
"protein_id": "ENSP00000261758.4",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 234,
"cds_start": 666,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015154.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261758.6"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "c.666G>A",
"hgvs_p": "p.Lys222Lys",
"transcript": "ENST00000561312.5",
"protein_id": "ENSP00000453430.1",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 234,
"cds_start": 666,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000561312.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "n.666G>A",
"hgvs_p": null,
"transcript": "ENST00000619987.4",
"protein_id": "ENSP00000482455.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000619987.4"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "c.702G>A",
"hgvs_p": "p.Lys234Lys",
"transcript": "ENST00000866863.1",
"protein_id": "ENSP00000536922.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 246,
"cds_start": 702,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866863.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "c.486G>A",
"hgvs_p": "p.Lys162Lys",
"transcript": "ENST00000866864.1",
"protein_id": "ENSP00000536923.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 174,
"cds_start": 486,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866864.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "c.483G>A",
"hgvs_p": "p.Lys161Lys",
"transcript": "ENST00000913247.1",
"protein_id": "ENSP00000583306.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 173,
"cds_start": 483,
"cds_end": null,
"cds_length": 522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913247.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "n.694G>A",
"hgvs_p": null,
"transcript": "NR_126327.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_126327.2"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "n.213+10321G>A",
"hgvs_p": null,
"transcript": "ENST00000422879.3",
"protein_id": "ENSP00000403839.3",
"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": "nonsense_mediated_decay",
"feature": "ENST00000422879.3"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "n.213+10321G>A",
"hgvs_p": null,
"transcript": "ENST00000559537.1",
"protein_id": "ENSP00000453220.1",
"transcript_support_level": 4,
"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": "nonsense_mediated_decay",
"feature": "ENST00000559537.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "n.241+10321G>A",
"hgvs_p": null,
"transcript": "NR_126328.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_126328.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"hgvs_c": "n.-118G>A",
"hgvs_p": null,
"transcript": "ENST00000560189.1",
"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": "pseudogene",
"feature": "ENST00000560189.1"
}
],
"gene_symbol": "MESD",
"gene_hgnc_id": 13520,
"dbsnp": "rs764715650",
"frequency_reference_population": 0.0000030982237,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.0000027367,
"gnomad_genomes_af": 0.00000656978,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"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": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.843,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_015154.3",
"gene_symbol": "MESD",
"hgnc_id": 13520,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.666G>A",
"hgvs_p": "p.Lys222Lys"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}