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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: 1-85276340-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=85276340&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 85276340,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000648566.1",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "c.13G>T",
"hgvs_p": "p.Ala5Ser",
"transcript": "NM_003921.5",
"protein_id": "NP_003912.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 233,
"cds_start": 13,
"cds_end": null,
"cds_length": 702,
"cdna_start": 293,
"cdna_end": null,
"cdna_length": 2833,
"mane_select": "ENST00000648566.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "c.13G>T",
"hgvs_p": "p.Ala5Ser",
"transcript": "ENST00000648566.1",
"protein_id": "ENSP00000498104.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 233,
"cds_start": 13,
"cds_end": null,
"cds_length": 702,
"cdna_start": 293,
"cdna_end": null,
"cdna_length": 2833,
"mane_select": "NM_003921.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "c.13G>T",
"hgvs_p": "p.Ala5Ser",
"transcript": "NM_001320715.2",
"protein_id": "NP_001307644.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 222,
"cds_start": 13,
"cds_end": null,
"cds_length": 669,
"cdna_start": 293,
"cdna_end": null,
"cdna_length": 2800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "c.13G>T",
"hgvs_p": "p.Ala5Ser",
"transcript": "ENST00000620248.3",
"protein_id": "ENSP00000480561.2",
"transcript_support_level": 5,
"aa_start": 5,
"aa_end": null,
"aa_length": 222,
"cds_start": 13,
"cds_end": null,
"cds_length": 669,
"cdna_start": 117,
"cdna_end": null,
"cdna_length": 1459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "n.13G>T",
"hgvs_p": null,
"transcript": "ENST00000649060.1",
"protein_id": "ENSP00000497490.1",
"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": 1561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "n.79G>T",
"hgvs_p": null,
"transcript": "ENST00000649434.1",
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "c.-325G>T",
"hgvs_p": null,
"transcript": "XM_011542397.4",
"protein_id": "XP_011540699.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 286,
"cds_start": -4,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "c.-1175G>T",
"hgvs_p": null,
"transcript": "XM_011542399.3",
"protein_id": "XP_011540701.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 215,
"cds_start": -4,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3966,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10-AS1",
"gene_hgnc_id": 55868,
"hgvs_c": "n.-48C>A",
"hgvs_p": null,
"transcript": "ENST00000654182.1",
"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": 2673,
"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": "BCL10-AS1",
"gene_hgnc_id": 55868,
"hgvs_c": "n.-249C>A",
"hgvs_p": null,
"transcript": "ENST00000791167.1",
"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": 766,
"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": "BCL10-AS1",
"gene_hgnc_id": 55868,
"hgvs_c": "n.-18C>A",
"hgvs_p": null,
"transcript": "NR_045484.1",
"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": 888,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"hgvs_c": "c.-325G>T",
"hgvs_p": null,
"transcript": "XM_011542398.3",
"protein_id": "XP_011540700.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 275,
"cds_start": -4,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BCL10",
"gene_hgnc_id": 989,
"dbsnp": "rs12037217",
"frequency_reference_population": 0.024588082,
"hom_count_reference_population": 780,
"allele_count_reference_population": 39674,
"gnomad_exomes_af": 0.0247372,
"gnomad_genomes_af": 0.023157,
"gnomad_exomes_ac": 36149,
"gnomad_genomes_ac": 3525,
"gnomad_exomes_homalt": 687,
"gnomad_genomes_homalt": 93,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.001587510108947754,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.039,
"revel_prediction": "Benign",
"alphamissense_score": 0.0874,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.77,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000648566.1",
"gene_symbol": "BCL10",
"hgnc_id": 989,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.13G>T",
"hgvs_p": "p.Ala5Ser"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_045484.1",
"gene_symbol": "BCL10-AS1",
"hgnc_id": 55868,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-18C>A",
"hgvs_p": null
}
],
"clinvar_disease": "BCL10-related disorder,Immunodeficiency 37,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Immunodeficiency 37|not provided|BCL10-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}