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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: 12-57796401-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57796401&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57796401,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000652027.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Leu266Ile",
"transcript": "NM_005726.6",
"protein_id": "NP_005717.3",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 325,
"cds_start": 796,
"cds_end": null,
"cds_length": 978,
"cdna_start": 811,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "ENST00000652027.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Leu266Ile",
"transcript": "ENST00000652027.2",
"protein_id": "ENSP00000499171.2",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 325,
"cds_start": 796,
"cds_end": null,
"cds_length": 978,
"cdna_start": 811,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "NM_005726.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.859C>A",
"hgvs_p": "p.Leu287Ile",
"transcript": "ENST00000323833.12",
"protein_id": "ENSP00000313877.8",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 346,
"cds_start": 859,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 885,
"cdna_end": null,
"cdna_length": 1218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.571+3328C>A",
"hgvs_p": null,
"transcript": "ENST00000543727.5",
"protein_id": "ENSP00000439342.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 215,
"cds_start": -4,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.859C>A",
"hgvs_p": "p.Leu287Ile",
"transcript": "NM_001172696.2",
"protein_id": "NP_001166167.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 346,
"cds_start": 859,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 874,
"cdna_end": null,
"cdna_length": 2060,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "n.*938C>A",
"hgvs_p": null,
"transcript": "ENST00000651066.1",
"protein_id": "ENSP00000499143.1",
"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": 2534,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257921",
"gene_hgnc_id": null,
"hgvs_c": "n.*425C>A",
"hgvs_p": null,
"transcript": "ENST00000651284.1",
"protein_id": "ENSP00000499064.1",
"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": 2246,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "n.*337C>A",
"hgvs_p": null,
"transcript": "ENST00000651899.1",
"protein_id": "ENSP00000498993.1",
"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": 1085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.*204C>A",
"hgvs_p": null,
"transcript": "NM_001172695.2",
"protein_id": "NP_001166166.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": -4,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.*204C>A",
"hgvs_p": null,
"transcript": "ENST00000540550.6",
"protein_id": "ENSP00000440987.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": -4,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1935,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "n.*938C>A",
"hgvs_p": null,
"transcript": "ENST00000651066.1",
"protein_id": "ENSP00000499143.1",
"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": 2534,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257921",
"gene_hgnc_id": null,
"hgvs_c": "n.*425C>A",
"hgvs_p": null,
"transcript": "ENST00000651284.1",
"protein_id": "ENSP00000499064.1",
"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": 2246,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "n.*337C>A",
"hgvs_p": null,
"transcript": "ENST00000651899.1",
"protein_id": "ENSP00000498993.1",
"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": 1085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.571+3328C>A",
"hgvs_p": null,
"transcript": "ENST00000550559.5",
"protein_id": "ENSP00000448575.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 230,
"cds_start": -4,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.571+3328C>A",
"hgvs_p": null,
"transcript": "NM_001172697.2",
"protein_id": "NP_001166168.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 215,
"cds_start": -4,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.571+3328C>A",
"hgvs_p": null,
"transcript": "ENST00000548851.5",
"protein_id": "ENSP00000450041.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 200,
"cds_start": -4,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "c.*140C>A",
"hgvs_p": null,
"transcript": "ENST00000457189.1",
"protein_id": "ENSP00000389162.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": -4,
"cds_end": null,
"cds_length": 506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 689,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"hgvs_c": "n.*34C>A",
"hgvs_p": null,
"transcript": "ENST00000497617.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TSFM",
"gene_hgnc_id": 12367,
"dbsnp": "rs62000432",
"frequency_reference_population": 0.0012230997,
"hom_count_reference_population": 31,
"allele_count_reference_population": 1960,
"gnomad_exomes_af": 0.00067648,
"gnomad_genomes_af": 0.00642675,
"gnomad_exomes_ac": 981,
"gnomad_genomes_ac": 979,
"gnomad_exomes_homalt": 19,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005405306816101074,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.164,
"revel_prediction": "Benign",
"alphamissense_score": 0.0805,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.922,
"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": "ENST00000652027.2",
"gene_symbol": "TSFM",
"hgnc_id": 12367,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.796C>A",
"hgvs_p": "p.Leu266Ile"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000651284.1",
"gene_symbol": "ENSG00000257921",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*425C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3,TSFM-related disorder,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "not provided|Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3|TSFM-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}