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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: 19-54108382-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=54108382&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 54108382,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_013342.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.367G>T",
"hgvs_p": "p.Val123Leu",
"transcript": "NM_013342.4",
"protein_id": "NP_037474.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 253,
"cds_start": 367,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000391759.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013342.4"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.367G>T",
"hgvs_p": "p.Val123Leu",
"transcript": "ENST00000391759.6",
"protein_id": "ENSP00000375639.1",
"transcript_support_level": 1,
"aa_start": 123,
"aa_end": null,
"aa_length": 253,
"cds_start": 367,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_013342.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000391759.6"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.340G>T",
"hgvs_p": "p.Val114Leu",
"transcript": "ENST00000391758.5",
"protein_id": "ENSP00000375638.1",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 244,
"cds_start": 340,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000391758.5"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.418G>T",
"hgvs_p": "p.Val140Leu",
"transcript": "ENST00000911296.1",
"protein_id": "ENSP00000581355.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 270,
"cds_start": 418,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911296.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.367G>T",
"hgvs_p": "p.Val123Leu",
"transcript": "ENST00000911297.1",
"protein_id": "ENSP00000581356.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 251,
"cds_start": 367,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911297.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.340G>T",
"hgvs_p": "p.Val114Leu",
"transcript": "NM_001321792.2",
"protein_id": "NP_001308721.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 244,
"cds_start": 340,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321792.2"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.367G>T",
"hgvs_p": "p.Val123Leu",
"transcript": "ENST00000391757.1",
"protein_id": "ENSP00000375637.1",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 193,
"cds_start": 367,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000391757.1"
},
{
"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": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "c.7G>T",
"hgvs_p": "p.Val3Leu",
"transcript": "XM_005278261.2",
"protein_id": "XP_005278318.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 133,
"cds_start": 7,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005278261.2"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NDUFA3",
"gene_hgnc_id": 7686,
"hgvs_c": "c.164-58C>A",
"hgvs_p": null,
"transcript": "ENST00000391764.7",
"protein_id": "ENSP00000375644.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 81,
"cds_start": null,
"cds_end": null,
"cds_length": 246,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000391764.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"hgvs_c": "n.296G>T",
"hgvs_p": null,
"transcript": "ENST00000420715.6",
"protein_id": "ENSP00000395180.1",
"transcript_support_level": 5,
"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": "ENST00000420715.6"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NDUFA3",
"gene_hgnc_id": 7686,
"hgvs_c": "n.*77-58C>A",
"hgvs_p": null,
"transcript": "ENST00000419113.5",
"protein_id": "ENSP00000398290.1",
"transcript_support_level": 3,
"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": "ENST00000419113.5"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NDUFA3",
"gene_hgnc_id": 7686,
"hgvs_c": "n.*199-58C>A",
"hgvs_p": null,
"transcript": "ENST00000422029.6",
"protein_id": "ENSP00000407335.1",
"transcript_support_level": 3,
"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": "ENST00000422029.6"
},
{
"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": "NDUFA3",
"gene_hgnc_id": 7686,
"hgvs_c": "n.-165C>A",
"hgvs_p": null,
"transcript": "ENST00000480713.1",
"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": "pseudogene",
"feature": "ENST00000480713.1"
}
],
"gene_symbol": "TFPT",
"gene_hgnc_id": 13630,
"dbsnp": "rs751160649",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.327201783657074,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.095,
"revel_prediction": "Benign",
"alphamissense_score": 0.7658,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.495,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_013342.4",
"gene_symbol": "TFPT",
"hgnc_id": 13630,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.367G>T",
"hgvs_p": "p.Val123Leu"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000391764.7",
"gene_symbol": "NDUFA3",
"hgnc_id": 7686,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.164-58C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}