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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: 4-186588765-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=186588765&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 186588765,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001440456.1",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.13594G>A",
"hgvs_p": "p.Val4532Ile",
"transcript": "NM_005245.4",
"protein_id": "NP_005236.2",
"transcript_support_level": null,
"aa_start": 4532,
"aa_end": null,
"aa_length": 4588,
"cds_start": 13594,
"cds_end": null,
"cds_length": 13767,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000441802.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005245.4"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.13594G>A",
"hgvs_p": "p.Val4532Ile",
"transcript": "ENST00000441802.7",
"protein_id": "ENSP00000406229.2",
"transcript_support_level": 5,
"aa_start": 4532,
"aa_end": null,
"aa_length": 4588,
"cds_start": 13594,
"cds_end": null,
"cds_length": 13767,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005245.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441802.7"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.13630G>A",
"hgvs_p": "p.Val4544Ile",
"transcript": "NM_001440456.1",
"protein_id": "NP_001427385.1",
"transcript_support_level": null,
"aa_start": 4544,
"aa_end": null,
"aa_length": 4600,
"cds_start": 13630,
"cds_end": null,
"cds_length": 13803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440456.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.13630G>A",
"hgvs_p": "p.Val4544Ile",
"transcript": "NM_001440457.1",
"protein_id": "NP_001427386.1",
"transcript_support_level": null,
"aa_start": 4544,
"aa_end": null,
"aa_length": 4600,
"cds_start": 13630,
"cds_end": null,
"cds_length": 13803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440457.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.13594G>A",
"hgvs_p": "p.Val4532Ile",
"transcript": "NM_001440455.1",
"protein_id": "NP_001427384.1",
"transcript_support_level": null,
"aa_start": 4532,
"aa_end": null,
"aa_length": 4588,
"cds_start": 13594,
"cds_end": null,
"cds_length": 13767,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440455.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.13594G>A",
"hgvs_p": "p.Val4532Ile",
"transcript": "ENST00000917425.1",
"protein_id": "ENSP00000587484.1",
"transcript_support_level": null,
"aa_start": 4532,
"aa_end": null,
"aa_length": 4588,
"cds_start": 13594,
"cds_end": null,
"cds_length": 13767,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917425.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.13588G>A",
"hgvs_p": "p.Val4530Ile",
"transcript": "ENST00000917424.1",
"protein_id": "ENSP00000587483.1",
"transcript_support_level": null,
"aa_start": 4530,
"aa_end": null,
"aa_length": 4586,
"cds_start": 13588,
"cds_end": null,
"cds_length": 13761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917424.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.931G>A",
"hgvs_p": "p.Val311Ile",
"transcript": "ENST00000512772.5",
"protein_id": "ENSP00000424157.1",
"transcript_support_level": 2,
"aa_start": 311,
"aa_end": null,
"aa_length": 367,
"cds_start": 931,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512772.5"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "n.1286G>A",
"hgvs_p": null,
"transcript": "ENST00000500085.2",
"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": "retained_intron",
"feature": "ENST00000500085.2"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.*42G>A",
"hgvs_p": null,
"transcript": "ENST00000507105.1",
"protein_id": "ENSP00000423801.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 283,
"cds_start": null,
"cds_end": null,
"cds_length": 853,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507105.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"hgvs_c": "c.*497G>A",
"hgvs_p": null,
"transcript": "ENST00000509537.1",
"protein_id": "ENSP00000421003.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 52,
"cds_start": null,
"cds_end": null,
"cds_length": 159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000509537.1"
}
],
"gene_symbol": "FAT1",
"gene_hgnc_id": 3595,
"dbsnp": "rs1394546790",
"frequency_reference_population": 0.0000012392326,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.8413e-7,
"gnomad_genomes_af": 0.00000657065,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08704802393913269,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.063,
"revel_prediction": "Benign",
"alphamissense_score": 0.0756,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.053,
"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": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001440456.1",
"gene_symbol": "FAT1",
"hgnc_id": 3595,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.13630G>A",
"hgvs_p": "p.Val4544Ile"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}