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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: 5-141641509-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=141641509&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "FCHSD1",
"hgnc_id": 25463,
"hgvs_c": "c.2062C>T",
"hgvs_p": "p.Pro688Ser",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_033449.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 27,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0671,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.63,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.010565221309661865,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 690,
"aa_ref": "P",
"aa_start": 688,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4319,
"cdna_start": 2112,
"cds_end": null,
"cds_length": 2073,
"cds_start": 2062,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_033449.3",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.2062C>T",
"hgvs_p": "p.Pro688Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000435817.7",
"protein_coding": true,
"protein_id": "NP_258260.1",
"strand": false,
"transcript": "NM_033449.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 690,
"aa_ref": "P",
"aa_start": 688,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4319,
"cdna_start": 2112,
"cds_end": null,
"cds_length": 2073,
"cds_start": 2062,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000435817.7",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.2062C>T",
"hgvs_p": "p.Pro688Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_033449.3",
"protein_coding": true,
"protein_id": "ENSP00000399259.2",
"strand": false,
"transcript": "ENST00000435817.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 726,
"aa_ref": "P",
"aa_start": 724,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2715,
"cdna_start": 2191,
"cds_end": null,
"cds_length": 2181,
"cds_start": 2170,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000896539.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.2170C>T",
"hgvs_p": "p.Pro724Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566598.1",
"strand": false,
"transcript": "ENST00000896539.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 688,
"aa_ref": "P",
"aa_start": 686,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4325,
"cdna_start": 2118,
"cds_end": null,
"cds_length": 2067,
"cds_start": 2056,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000896537.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.2056C>T",
"hgvs_p": "p.Pro686Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566596.1",
"strand": false,
"transcript": "ENST00000896537.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 645,
"aa_ref": "P",
"aa_start": 643,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2477,
"cdna_start": 1955,
"cds_end": null,
"cds_length": 1938,
"cds_start": 1927,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000896538.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.1927C>T",
"hgvs_p": "p.Pro643Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566597.1",
"strand": false,
"transcript": "ENST00000896538.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 634,
"aa_ref": "P",
"aa_start": 632,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2471,
"cdna_start": 1945,
"cds_end": null,
"cds_length": 1905,
"cds_start": 1894,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000969298.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.1894C>T",
"hgvs_p": "p.Pro632Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639357.1",
"strand": false,
"transcript": "ENST00000969298.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 616,
"aa_ref": "P",
"aa_start": 614,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4089,
"cdna_start": 1889,
"cds_end": null,
"cds_length": 1851,
"cds_start": 1840,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000969297.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.1840C>T",
"hgvs_p": "p.Pro614Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639356.1",
"strand": false,
"transcript": "ENST00000969297.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 688,
"aa_ref": "P",
"aa_start": 686,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4313,
"cdna_start": 2106,
"cds_end": null,
"cds_length": 2067,
"cds_start": 2056,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_005268524.6",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.2056C>T",
"hgvs_p": "p.Pro686Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005268581.1",
"strand": false,
"transcript": "XM_005268524.6",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 647,
"aa_ref": "P",
"aa_start": 645,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4190,
"cdna_start": 1983,
"cds_end": null,
"cds_length": 1944,
"cds_start": 1933,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_006714803.5",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.1933C>T",
"hgvs_p": "p.Pro645Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006714866.1",
"strand": false,
"transcript": "XM_006714803.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 645,
"aa_ref": "P",
"aa_start": 643,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4184,
"cdna_start": 1977,
"cds_end": null,
"cds_length": 1938,
"cds_start": 1927,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_047417860.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.1927C>T",
"hgvs_p": "p.Pro643Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273816.1",
"strand": false,
"transcript": "XM_047417860.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 598,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2477,
"cdna_start": null,
"cds_end": null,
"cds_length": 1797,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000522783.5",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.*150C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000428677.1",
"strand": false,
"transcript": "ENST00000522783.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 719,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000518160.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "n.419C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000518160.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3181,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000520747.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "n.975C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000520747.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2577,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000522126.5",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "n.*619C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000427796.1",
"strand": false,
"transcript": "ENST00000522126.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3932,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000523856.5",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "n.1731C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000523856.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2577,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "ENST00000522126.5",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "n.*619C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000427796.1",
"strand": false,
"transcript": "ENST00000522126.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 632,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1969,
"cdna_start": null,
"cds_end": null,
"cds_length": 1899,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047417861.1",
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"hgvs_c": "c.*213C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273817.1",
"strand": true,
"transcript": "XM_047417861.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs560798832",
"effect": "missense_variant",
"frequency_reference_population": 0.000017967348,
"gene_hgnc_id": 25463,
"gene_symbol": "FCHSD1",
"gnomad_exomes_ac": 24,
"gnomad_exomes_af": 0.0000177725,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000196951,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.311,
"pos": 141641509,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.022,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_033449.3"
}
]
}