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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: 3-10039727-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=10039727&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 10039727,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000675286.1",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "NM_001018115.3",
"protein_id": "NP_001018125.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1451,
"cds_start": 577,
"cds_end": null,
"cds_length": 4356,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 5096,
"mane_select": "ENST00000675286.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "ENST00000675286.1",
"protein_id": "ENSP00000502379.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1451,
"cds_start": 577,
"cds_end": null,
"cds_length": 4356,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 5096,
"mane_select": "NM_001018115.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "ENST00000287647.7",
"protein_id": "ENSP00000287647.3",
"transcript_support_level": 1,
"aa_start": 193,
"aa_end": null,
"aa_length": 1471,
"cds_start": 577,
"cds_end": null,
"cds_length": 4416,
"cdna_start": 670,
"cdna_end": null,
"cdna_length": 5219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "ENST00000419585.5",
"protein_id": "ENSP00000398754.1",
"transcript_support_level": 1,
"aa_start": 193,
"aa_end": null,
"aa_length": 1451,
"cds_start": 577,
"cds_end": null,
"cds_length": 4356,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 5185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "ENST00000431693.1",
"protein_id": "ENSP00000399354.1",
"transcript_support_level": 1,
"aa_start": 193,
"aa_end": null,
"aa_length": 241,
"cds_start": 577,
"cds_end": null,
"cds_length": 726,
"cdna_start": 615,
"cdna_end": null,
"cdna_length": 2450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "NM_033084.6",
"protein_id": "NP_149075.2",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1471,
"cds_start": 577,
"cds_end": null,
"cds_length": 4416,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 4879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "NM_001374254.1",
"protein_id": "NP_001361183.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1458,
"cds_start": 577,
"cds_end": null,
"cds_length": 4377,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 4840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "NM_001319984.2",
"protein_id": "NP_001306913.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1451,
"cds_start": 577,
"cds_end": null,
"cds_length": 4356,
"cdna_start": 800,
"cdna_end": null,
"cdna_length": 5249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "NM_001374253.1",
"protein_id": "NP_001361182.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1414,
"cds_start": 577,
"cds_end": null,
"cds_length": 4245,
"cdna_start": 647,
"cdna_end": null,
"cdna_length": 4985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "ENST00000676013.1",
"protein_id": "ENSP00000501999.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 1413,
"cds_start": 577,
"cds_end": null,
"cds_length": 4244,
"cdna_start": 667,
"cdna_end": null,
"cdna_length": 4334,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala",
"transcript": "NM_001374255.1",
"protein_id": "NP_001361184.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 232,
"cds_start": 577,
"cds_end": null,
"cds_length": 699,
"cdna_start": 800,
"cdna_end": null,
"cdna_length": 1068,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "n.292A>G",
"hgvs_p": null,
"transcript": "ENST00000438741.1",
"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": 558,
"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": 10,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "n.*585A>G",
"hgvs_p": null,
"transcript": "ENST00000682647.1",
"protein_id": "ENSP00000506736.1",
"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": 2145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "n.*585A>G",
"hgvs_p": null,
"transcript": "ENST00000682647.1",
"protein_id": "ENSP00000506736.1",
"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": 2145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"dbsnp": "rs34936017",
"frequency_reference_population": 0.0026870095,
"hom_count_reference_population": 106,
"allele_count_reference_population": 4337,
"gnomad_exomes_af": 0.00274445,
"gnomad_genomes_af": 0.00213529,
"gnomad_exomes_ac": 4012,
"gnomad_genomes_ac": 325,
"gnomad_exomes_homalt": 97,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0030479729175567627,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.13,
"revel_prediction": "Benign",
"alphamissense_score": 0.0837,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.448,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000675286.1",
"gene_symbol": "FANCD2",
"hgnc_id": 3585,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.577A>G",
"hgvs_p": "p.Thr193Ala"
}
],
"clinvar_disease": "Fanconi anemia,Fanconi anemia complementation group D2,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:4 O:1",
"phenotype_combined": "not specified|not provided|Fanconi anemia|Fanconi anemia complementation group D2",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}