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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: 13-113140972-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=113140972&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 113140972,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000504.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys",
"transcript": "NM_000504.4",
"protein_id": "NP_000495.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 488,
"cds_start": 424,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000375559.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000504.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys",
"transcript": "ENST00000375559.8",
"protein_id": "ENSP00000364709.3",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 488,
"cds_start": 424,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000504.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375559.8"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys",
"transcript": "ENST00000375551.7",
"protein_id": "ENSP00000364701.3",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 332,
"cds_start": 424,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375551.7"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "n.*383G>A",
"hgvs_p": null,
"transcript": "ENST00000410083.6",
"protein_id": "ENSP00000386320.2",
"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": "ENST00000410083.6"
},
{
"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": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "n.461G>A",
"hgvs_p": null,
"transcript": "ENST00000477269.5",
"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": "ENST00000477269.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "n.*383G>A",
"hgvs_p": null,
"transcript": "ENST00000410083.6",
"protein_id": "ENSP00000386320.2",
"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": "ENST00000410083.6"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys",
"transcript": "ENST00000858583.1",
"protein_id": "ENSP00000528642.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 493,
"cds_start": 424,
"cds_end": null,
"cds_length": 1482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858583.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys",
"transcript": "ENST00000858582.1",
"protein_id": "ENSP00000528641.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 491,
"cds_start": 424,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858582.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys",
"transcript": "ENST00000409306.5",
"protein_id": "ENSP00000387092.1",
"transcript_support_level": 3,
"aa_start": 142,
"aa_end": null,
"aa_length": 334,
"cds_start": 424,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409306.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys",
"transcript": "NM_001312675.2",
"protein_id": "NP_001299604.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 332,
"cds_start": 424,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001312675.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.370+1502G>A",
"hgvs_p": null,
"transcript": "NM_001312674.2",
"protein_id": "NP_001299603.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 444,
"cds_start": null,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001312674.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "c.370+1502G>A",
"hgvs_p": null,
"transcript": "ENST00000858581.1",
"protein_id": "ENSP00000528640.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 444,
"cds_start": null,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858581.1"
},
{
"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": "F10",
"gene_hgnc_id": 3528,
"hgvs_c": "n.453G>A",
"hgvs_p": null,
"transcript": "ENST00000498455.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000498455.1"
}
],
"gene_symbol": "F10",
"gene_hgnc_id": 3528,
"dbsnp": "rs61753266",
"frequency_reference_population": 0.0037580337,
"hom_count_reference_population": 22,
"allele_count_reference_population": 6066,
"gnomad_exomes_af": 0.00380562,
"gnomad_genomes_af": 0.00330148,
"gnomad_exomes_ac": 5563,
"gnomad_genomes_ac": 503,
"gnomad_exomes_homalt": 20,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05869060754776001,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.614,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1876,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.474,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000504.4",
"gene_symbol": "F10",
"hgnc_id": 3528,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.424G>A",
"hgvs_p": "p.Glu142Lys"
}
],
"clinvar_disease": "Abnormal bleeding,F10-related disorder,Factor X deficiency,Hereditary factor X deficiency disease,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:4 LB:3",
"phenotype_combined": "Factor X deficiency|not specified|not provided|Abnormal bleeding|Hereditary factor X deficiency disease|F10-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}