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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: 15-44711548-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=44711548&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 44711548,
"ref": "T",
"alt": "C",
"effect": "start_lost",
"transcript": "ENST00000648006.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_004048.4",
"protein_id": "NP_004039.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 119,
"cds_start": 2,
"cds_end": null,
"cds_length": 360,
"cdna_start": 32,
"cdna_end": null,
"cdna_length": 943,
"mane_select": "ENST00000648006.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000648006.3",
"protein_id": "ENSP00000497910.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 119,
"cds_start": 2,
"cds_end": null,
"cds_length": 360,
"cdna_start": 32,
"cdna_end": null,
"cdna_length": 943,
"mane_select": "NM_004048.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000559916.1",
"protein_id": "ENSP00000453350.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 119,
"cds_start": 2,
"cds_end": null,
"cds_length": 360,
"cdna_start": 36,
"cdna_end": null,
"cdna_length": 1081,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000557901.5",
"protein_id": "ENSP00000452861.1",
"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": 407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "XM_005254549.4",
"protein_id": "XP_005254606.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 122,
"cds_start": 2,
"cds_end": null,
"cds_length": 369,
"cdna_start": 32,
"cdna_end": null,
"cdna_length": 977,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000349264.10",
"protein_id": "ENSP00000340858.6",
"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": 732,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "n.62T>C",
"hgvs_p": null,
"transcript": "ENST00000559720.5",
"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": 1220,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000561424.5",
"protein_id": "ENSP00000453191.1",
"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": 604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"hgvs_c": "n.83+108T>C",
"hgvs_p": null,
"transcript": "ENST00000695792.1",
"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": 925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-782A>G",
"hgvs_p": null,
"transcript": "NM_001387263.1",
"protein_id": "NP_001374192.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 543,
"cds_start": -4,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": "ENST00000682850.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-782A>G",
"hgvs_p": null,
"transcript": "ENST00000682850.1",
"protein_id": "ENSP00000508024.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 543,
"cds_start": -4,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": "NM_001387263.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-604A>G",
"hgvs_p": null,
"transcript": "NM_001387261.1",
"protein_id": "NP_001374190.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 543,
"cds_start": -4,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-872A>G",
"hgvs_p": null,
"transcript": "NM_001387262.1",
"protein_id": "NP_001374191.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 543,
"cds_start": -4,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-292A>G",
"hgvs_p": null,
"transcript": "NM_001387260.1",
"protein_id": "NP_001374189.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 512,
"cds_start": -4,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1894,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "n.-232A>G",
"hgvs_p": null,
"transcript": "ENST00000558573.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-782A>G",
"hgvs_p": null,
"transcript": "XM_011521338.4",
"protein_id": "XP_011519640.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 565,
"cds_start": -4,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-663A>G",
"hgvs_p": null,
"transcript": "XM_011521339.4",
"protein_id": "XP_011519641.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 565,
"cds_start": -4,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2193,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-872A>G",
"hgvs_p": null,
"transcript": "XM_047432230.1",
"protein_id": "XP_047288186.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 565,
"cds_start": -4,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-866A>G",
"hgvs_p": null,
"transcript": "XM_011521343.4",
"protein_id": "XP_011519645.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 481,
"cds_start": -4,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PATL2",
"gene_hgnc_id": 33630,
"hgvs_c": "c.-837A>G",
"hgvs_p": null,
"transcript": "XM_011521345.4",
"protein_id": "XP_011519647.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 478,
"cds_start": -4,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "B2M",
"gene_hgnc_id": 914,
"dbsnp": "rs1057519879",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9776127934455872,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.188,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.606,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000648006.3",
"gene_symbol": "B2M",
"hgnc_id": 914,
"effects": [
"start_lost"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000682850.1",
"gene_symbol": "PATL2",
"hgnc_id": 33630,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-782A>G",
"hgvs_p": null
}
],
"clinvar_disease": " hereditary systemic 6, hypercatabolic,Amyloidosis,Hypoproteinemia",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Amyloidosis, hereditary systemic 6;Hypoproteinemia, hypercatabolic",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}