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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: 19-1468494-G-GC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1468494&ref=G&alt=GC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 1468494,
"ref": "G",
"alt": "GC",
"effect": "frameshift_variant",
"transcript": "ENST00000590469.6",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5199dupC",
"hgvs_p": "p.Lys1734fs",
"transcript": "NM_005883.3",
"protein_id": "NP_005874.1",
"transcript_support_level": null,
"aa_start": 1734,
"aa_end": null,
"aa_length": 2303,
"cds_start": 5200,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 5436,
"cdna_end": null,
"cdna_length": 10179,
"mane_select": "ENST00000590469.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5199dupC",
"hgvs_p": "p.Lys1734fs",
"transcript": "ENST00000590469.6",
"protein_id": "ENSP00000467073.2",
"transcript_support_level": 1,
"aa_start": 1734,
"aa_end": null,
"aa_length": 2303,
"cds_start": 5200,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 5436,
"cdna_end": null,
"cdna_length": 10179,
"mane_select": "NM_005883.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5199dupC",
"hgvs_p": "p.Lys1734fs",
"transcript": "ENST00000233607.6",
"protein_id": "ENSP00000233607.2",
"transcript_support_level": 1,
"aa_start": 1734,
"aa_end": null,
"aa_length": 2303,
"cds_start": 5200,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 5408,
"cdna_end": null,
"cdna_length": 10151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5199dupC",
"hgvs_p": "p.Lys1734fs",
"transcript": "ENST00000535453.5",
"protein_id": "ENSP00000442954.1",
"transcript_support_level": 1,
"aa_start": 1734,
"aa_end": null,
"aa_length": 2303,
"cds_start": 5200,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 6913,
"cdna_end": null,
"cdna_length": 11656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "C19orf25",
"gene_hgnc_id": 26711,
"hgvs_c": "c.131-6671dupG",
"hgvs_p": null,
"transcript": "ENST00000588427.5",
"protein_id": "ENSP00000468000.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 71,
"cds_start": -4,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5196dupC",
"hgvs_p": "p.Lys1733fs",
"transcript": "NM_001351273.1",
"protein_id": "NP_001338202.1",
"transcript_support_level": null,
"aa_start": 1733,
"aa_end": null,
"aa_length": 2302,
"cds_start": 5197,
"cds_end": null,
"cds_length": 6909,
"cdna_start": 5215,
"cdna_end": null,
"cdna_length": 9958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5271dupC",
"hgvs_p": "p.Lys1758fs",
"transcript": "XM_005259475.3",
"protein_id": "XP_005259532.1",
"transcript_support_level": null,
"aa_start": 1758,
"aa_end": null,
"aa_length": 2327,
"cds_start": 5272,
"cds_end": null,
"cds_length": 6984,
"cdna_start": 5330,
"cdna_end": null,
"cdna_length": 10073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5268dupC",
"hgvs_p": "p.Lys1757fs",
"transcript": "XM_006722607.3",
"protein_id": "XP_006722670.1",
"transcript_support_level": null,
"aa_start": 1757,
"aa_end": null,
"aa_length": 2326,
"cds_start": 5269,
"cds_end": null,
"cds_length": 6981,
"cdna_start": 5327,
"cdna_end": null,
"cdna_length": 10070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5199dupC",
"hgvs_p": "p.Lys1734fs",
"transcript": "XM_006722608.4",
"protein_id": "XP_006722671.3",
"transcript_support_level": null,
"aa_start": 1734,
"aa_end": null,
"aa_length": 2303,
"cds_start": 5200,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 5428,
"cdna_end": null,
"cdna_length": 10171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5199dupC",
"hgvs_p": "p.Lys1734fs",
"transcript": "XM_006722609.4",
"protein_id": "XP_006722672.1",
"transcript_support_level": null,
"aa_start": 1734,
"aa_end": null,
"aa_length": 2303,
"cds_start": 5200,
"cds_end": null,
"cds_length": 6912,
"cdna_start": 5336,
"cdna_end": null,
"cdna_length": 10079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5196dupC",
"hgvs_p": "p.Lys1733fs",
"transcript": "XM_006722610.4",
"protein_id": "XP_006722673.3",
"transcript_support_level": null,
"aa_start": 1733,
"aa_end": null,
"aa_length": 2302,
"cds_start": 5197,
"cds_end": null,
"cds_length": 6909,
"cdna_start": 5425,
"cdna_end": null,
"cdna_length": 10168,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5196dupC",
"hgvs_p": "p.Lys1733fs",
"transcript": "XM_047438031.1",
"protein_id": "XP_047293987.1",
"transcript_support_level": null,
"aa_start": 1733,
"aa_end": null,
"aa_length": 2302,
"cds_start": 5197,
"cds_end": null,
"cds_length": 6909,
"cdna_start": 5433,
"cdna_end": null,
"cdna_length": 10176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.5196dupC",
"hgvs_p": "p.Lys1733fs",
"transcript": "XM_047438032.1",
"protein_id": "XP_047293988.1",
"transcript_support_level": null,
"aa_start": 1733,
"aa_end": null,
"aa_length": 2302,
"cds_start": 5197,
"cds_end": null,
"cds_length": 6909,
"cdna_start": 5333,
"cdna_end": null,
"cdna_length": 10076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"dbsnp": "rs886040957",
"frequency_reference_population": 0.0000013768378,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137684,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.053,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000590469.6",
"gene_symbol": "APC2",
"hgnc_id": 24036,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.5199dupC",
"hgvs_p": "p.Lys1734fs"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000588427.5",
"gene_symbol": "C19orf25",
"hgnc_id": 26711,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.131-6671dupG",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 74,Intellectual developmental disorder",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Intellectual developmental disorder, autosomal recessive 74",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}