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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: 1-212858492-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=212858492&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 212858492,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000366971.9",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Pro14Ser",
"transcript": "NM_014053.4",
"protein_id": "NP_054772.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 555,
"cds_start": 40,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 5919,
"mane_select": "ENST00000366971.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Pro14Ser",
"transcript": "ENST00000366971.9",
"protein_id": "ENSP00000355938.4",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 555,
"cds_start": 40,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 5919,
"mane_select": "NM_014053.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Pro14Ser",
"transcript": "XM_011509447.3",
"protein_id": "XP_011507749.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 365,
"cds_start": 40,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 1408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Pro14Ser",
"transcript": "XM_011509448.2",
"protein_id": "XP_011507750.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 365,
"cds_start": 40,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 1405,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "n.218C>T",
"hgvs_p": null,
"transcript": "XR_007059232.1",
"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": 5551,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "n.218C>T",
"hgvs_p": null,
"transcript": "XR_247024.4",
"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": 5662,
"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": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "n.218C>T",
"hgvs_p": null,
"transcript": "XR_426771.2",
"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": 1397,
"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": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "n.218C>T",
"hgvs_p": null,
"transcript": "XR_426772.4",
"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": 1281,
"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": "FLVCR1",
"gene_hgnc_id": 24682,
"hgvs_c": "n.218C>T",
"hgvs_p": null,
"transcript": "XR_921769.2",
"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": 1278,
"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": "FLVCR1-DT",
"gene_hgnc_id": 39077,
"hgvs_c": "n.-183G>A",
"hgvs_p": null,
"transcript": "ENST00000426161.9",
"protein_id": null,
"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": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FLVCR1",
"gene_hgnc_id": 24682,
"dbsnp": "rs111734301",
"frequency_reference_population": 0.000057422756,
"hom_count_reference_population": 1,
"allele_count_reference_population": 83,
"gnomad_exomes_af": 0.0000324793,
"gnomad_genomes_af": 0.000269223,
"gnomad_exomes_ac": 42,
"gnomad_genomes_ac": 41,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009815007448196411,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.076,
"revel_prediction": "Benign",
"alphamissense_score": 0.0704,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.184,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000366971.9",
"gene_symbol": "FLVCR1",
"hgnc_id": 24682,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Pro14Ser"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000426161.9",
"gene_symbol": "FLVCR1-DT",
"hgnc_id": 39077,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-183G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}