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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: 16-74716507-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=74716507&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 74716507,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_024306.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "c.879C>T",
"hgvs_p": "p.Pro293Pro",
"transcript": "NM_024306.5",
"protein_id": "NP_077282.3",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 372,
"cds_start": 879,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000219368.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024306.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "c.879C>T",
"hgvs_p": "p.Pro293Pro",
"transcript": "ENST00000219368.8",
"protein_id": "ENSP00000219368.3",
"transcript_support_level": 1,
"aa_start": 293,
"aa_end": null,
"aa_length": 372,
"cds_start": 879,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024306.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000219368.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "n.600C>T",
"hgvs_p": null,
"transcript": "ENST00000562145.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000562145.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "c.873C>T",
"hgvs_p": "p.Pro291Pro",
"transcript": "ENST00000888352.1",
"protein_id": "ENSP00000558411.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 370,
"cds_start": 873,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888352.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "c.798C>T",
"hgvs_p": "p.Pro266Pro",
"transcript": "ENST00000888351.1",
"protein_id": "ENSP00000558410.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 345,
"cds_start": 798,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888351.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "c.639C>T",
"hgvs_p": "p.Pro213Pro",
"transcript": "XM_011523319.3",
"protein_id": "XP_011521621.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 292,
"cds_start": 639,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011523319.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "c.*1743C>T",
"hgvs_p": null,
"transcript": "XM_011523317.4",
"protein_id": "XP_011521619.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 369,
"cds_start": null,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011523317.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "n.*158C>T",
"hgvs_p": null,
"transcript": "ENST00000567683.5",
"protein_id": "ENSP00000455126.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000567683.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"hgvs_c": "n.*158C>T",
"hgvs_p": null,
"transcript": "ENST00000567683.5",
"protein_id": "ENSP00000455126.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000567683.5"
}
],
"gene_symbol": "FA2H",
"gene_hgnc_id": 21197,
"dbsnp": "rs2301865",
"frequency_reference_population": 0.796887,
"hom_count_reference_population": 514126,
"allele_count_reference_population": 1285307,
"gnomad_exomes_af": 0.799301,
"gnomad_genomes_af": 0.773635,
"gnomad_exomes_ac": 1167962,
"gnomad_genomes_ac": 117345,
"gnomad_exomes_homalt": 468526,
"gnomad_genomes_homalt": 45600,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.577,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_024306.5",
"gene_symbol": "FA2H",
"hgnc_id": 21197,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.879C>T",
"hgvs_p": "p.Pro293Pro"
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 35,Spastic paraplegia,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:9",
"phenotype_combined": "not specified|Hereditary spastic paraplegia 35|Spastic paraplegia|not provided|Hereditary spastic paraplegia",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}