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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: 6-6318562-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=6318562&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 6318562,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000129.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.103G>T",
"hgvs_p": "p.Val35Leu",
"transcript": "NM_000129.4",
"protein_id": "NP_000120.2",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 732,
"cds_start": 103,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264870.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000129.4"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.103G>T",
"hgvs_p": "p.Val35Leu",
"transcript": "ENST00000264870.8",
"protein_id": "ENSP00000264870.3",
"transcript_support_level": 1,
"aa_start": 35,
"aa_end": null,
"aa_length": 732,
"cds_start": 103,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000129.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264870.8"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.103G>T",
"hgvs_p": "p.Val35Leu",
"transcript": "ENST00000950947.1",
"protein_id": "ENSP00000621006.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 732,
"cds_start": 103,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950947.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.103G>T",
"hgvs_p": "p.Val35Leu",
"transcript": "ENST00000878383.1",
"protein_id": "ENSP00000548442.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 669,
"cds_start": 103,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878383.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.103G>T",
"hgvs_p": "p.Val35Leu",
"transcript": "ENST00000950946.1",
"protein_id": "ENSP00000621005.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 648,
"cds_start": 103,
"cds_end": null,
"cds_length": 1947,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950946.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.265G>T",
"hgvs_p": "p.Val89Leu",
"transcript": "ENST00000431222.6",
"protein_id": "ENSP00000416295.2",
"transcript_support_level": 4,
"aa_start": 89,
"aa_end": null,
"aa_length": 184,
"cds_start": 265,
"cds_end": null,
"cds_length": 557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000431222.6"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.175G>T",
"hgvs_p": "p.Val59Leu",
"transcript": "ENST00000451619.1",
"protein_id": "ENSP00000411114.1",
"transcript_support_level": 2,
"aa_start": 59,
"aa_end": null,
"aa_length": 146,
"cds_start": 175,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000451619.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"hgvs_c": "c.103G>T",
"hgvs_p": "p.Val35Leu",
"transcript": "ENST00000414279.5",
"protein_id": "ENSP00000413334.1",
"transcript_support_level": 4,
"aa_start": 35,
"aa_end": null,
"aa_length": 137,
"cds_start": 103,
"cds_end": null,
"cds_length": 416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000414279.5"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000309672",
"gene_hgnc_id": null,
"hgvs_c": "n.65-11191C>A",
"hgvs_p": null,
"transcript": "ENST00000842908.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000842908.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124901253",
"gene_hgnc_id": null,
"hgvs_c": "n.55-11191C>A",
"hgvs_p": null,
"transcript": "XR_007059428.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "XR_007059428.1"
}
],
"gene_symbol": "F13A1",
"gene_hgnc_id": 3531,
"dbsnp": "rs5985",
"frequency_reference_population": 0.23308824,
"hom_count_reference_population": 46576,
"allele_count_reference_population": 376031,
"gnomad_exomes_af": 0.234965,
"gnomad_genomes_af": 0.215039,
"gnomad_exomes_ac": 343358,
"gnomad_genomes_ac": 32673,
"gnomad_exomes_homalt": 42791,
"gnomad_genomes_homalt": 3785,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00582548975944519,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.216,
"revel_prediction": "Benign",
"alphamissense_score": 0.0575,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.148,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000129.4",
"gene_symbol": "F13A1",
"hgnc_id": 3531,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.103G>T",
"hgvs_p": "p.Val35Leu"
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000842908.1",
"gene_symbol": "ENSG00000309672",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.65-11191C>A",
"hgvs_p": null
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_007059428.1",
"gene_symbol": "LOC124901253",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.55-11191C>A",
"hgvs_p": null
}
],
"clinvar_disease": " A subunit, deficiency of, protection against,Factor XIII,Myocardial infarction,Venous thrombosis,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:3",
"phenotype_combined": "Venous thrombosis, protection against|Myocardial infarction, protection against|not specified|Factor XIII, A subunit, deficiency of|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}