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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: 19-680361-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=680361&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 680361,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005860.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSTL3",
"gene_hgnc_id": 3973,
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ser126Leu",
"transcript": "NM_005860.3",
"protein_id": "NP_005851.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 263,
"cds_start": 377,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000166139.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005860.3"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSTL3",
"gene_hgnc_id": 3973,
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ser126Leu",
"transcript": "ENST00000166139.9",
"protein_id": "ENSP00000166139.3",
"transcript_support_level": 1,
"aa_start": 126,
"aa_end": null,
"aa_length": 263,
"cds_start": 377,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005860.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000166139.9"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSTL3",
"gene_hgnc_id": 3973,
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ser126Leu",
"transcript": "ENST00000905299.1",
"protein_id": "ENSP00000575358.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 187,
"cds_start": 377,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905299.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSTL3",
"gene_hgnc_id": 3973,
"hgvs_c": "c.44C>T",
"hgvs_p": "p.Ser15Leu",
"transcript": "ENST00000589185.2",
"protein_id": "ENSP00000484376.1",
"transcript_support_level": 2,
"aa_start": 15,
"aa_end": null,
"aa_length": 83,
"cds_start": 44,
"cds_end": null,
"cds_length": 253,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000589185.2"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "FSTL3",
"gene_hgnc_id": 3973,
"hgvs_c": "c.104-1289C>T",
"hgvs_p": null,
"transcript": "ENST00000964202.1",
"protein_id": "ENSP00000634261.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 53,
"cds_start": null,
"cds_end": null,
"cds_length": 162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000964202.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FSTL3",
"gene_hgnc_id": 3973,
"hgvs_c": "n.111C>T",
"hgvs_p": null,
"transcript": "ENST00000592058.3",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000592058.3"
}
],
"gene_symbol": "FSTL3",
"gene_hgnc_id": 3973,
"dbsnp": "rs768914737",
"frequency_reference_population": 0.000106981104,
"hom_count_reference_population": 0,
"allele_count_reference_population": 137,
"gnomad_exomes_af": 0.000115167,
"gnomad_genomes_af": 0.0000461121,
"gnomad_exomes_ac": 130,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.49944132566452026,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.207,
"revel_prediction": "Benign",
"alphamissense_score": 0.1173,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.57,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_005860.3",
"gene_symbol": "FSTL3",
"hgnc_id": 3973,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.377C>T",
"hgvs_p": "p.Ser126Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}