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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: 2-159879264-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=159879264&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 159879264,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001198759.1",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75",
"gene_hgnc_id": 6729,
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn",
"transcript": "NM_002349.4",
"protein_id": "NP_002340.2",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 1722,
"cds_start": 1510,
"cds_end": null,
"cds_length": 5169,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263636.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002349.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75",
"gene_hgnc_id": 6729,
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn",
"transcript": "ENST00000263636.5",
"protein_id": "ENSP00000263636.4",
"transcript_support_level": 1,
"aa_start": 504,
"aa_end": null,
"aa_length": 1722,
"cds_start": 1510,
"cds_end": null,
"cds_length": 5169,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002349.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263636.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75-CD302",
"gene_hgnc_id": 38828,
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn",
"transcript": "ENST00000504764.5",
"protein_id": "ENSP00000423463.1",
"transcript_support_level": 2,
"aa_start": 504,
"aa_end": null,
"aa_length": 1873,
"cds_start": 1510,
"cds_end": null,
"cds_length": 5622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504764.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75",
"gene_hgnc_id": 6729,
"hgvs_c": "n.1570G>A",
"hgvs_p": null,
"transcript": "ENST00000484559.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000484559.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75-CD302",
"gene_hgnc_id": 38828,
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn",
"transcript": "NM_001198759.1",
"protein_id": "NP_001185688.1",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 1873,
"cds_start": 1510,
"cds_end": null,
"cds_length": 5622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198759.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75-CD302",
"gene_hgnc_id": 38828,
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn",
"transcript": "NM_001198760.1",
"protein_id": "NP_001185689.1",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 1817,
"cds_start": 1510,
"cds_end": null,
"cds_length": 5454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198760.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75-CD302",
"gene_hgnc_id": 38828,
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn",
"transcript": "ENST00000505052.1",
"protein_id": "ENSP00000421035.1",
"transcript_support_level": 2,
"aa_start": 504,
"aa_end": null,
"aa_length": 1817,
"cds_start": 1510,
"cds_end": null,
"cds_length": 5454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505052.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75",
"gene_hgnc_id": 6729,
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn",
"transcript": "ENST00000971950.1",
"protein_id": "ENSP00000642009.1",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 1672,
"cds_start": 1510,
"cds_end": null,
"cds_length": 5019,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971950.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LY75",
"gene_hgnc_id": 6729,
"hgvs_c": "c.1138G>A",
"hgvs_p": "p.Asp380Asn",
"transcript": "ENST00000971951.1",
"protein_id": "ENSP00000642010.1",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 1598,
"cds_start": 1138,
"cds_end": null,
"cds_length": 4797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971951.1"
}
],
"gene_symbol": "LY75-CD302",
"gene_hgnc_id": 38828,
"dbsnp": "rs77761086",
"frequency_reference_population": 0.0008343921,
"hom_count_reference_population": 12,
"allele_count_reference_population": 1345,
"gnomad_exomes_af": 0.000456271,
"gnomad_genomes_af": 0.00445854,
"gnomad_exomes_ac": 666,
"gnomad_genomes_ac": 679,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 7,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0041893720626831055,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.068,
"revel_prediction": "Benign",
"alphamissense_score": 0.0681,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.119,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001198759.1",
"gene_symbol": "LY75-CD302",
"hgnc_id": 38828,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn"
},
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002349.4",
"gene_symbol": "LY75",
"hgnc_id": 6729,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1510G>A",
"hgvs_p": "p.Asp504Asn"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}