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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: 8-132180246-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=132180246&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 132180246,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_004519.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Arg230Cys",
"transcript": "NM_004519.4",
"protein_id": "NP_004510.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 872,
"cds_start": 688,
"cds_end": null,
"cds_length": 2619,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000388996.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004519.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Arg230Cys",
"transcript": "ENST00000388996.10",
"protein_id": "ENSP00000373648.3",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 872,
"cds_start": 688,
"cds_end": null,
"cds_length": 2619,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004519.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000388996.10"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Arg230Cys",
"transcript": "ENST00000519445.5",
"protein_id": "ENSP00000428790.1",
"transcript_support_level": 5,
"aa_start": 230,
"aa_end": null,
"aa_length": 860,
"cds_start": 688,
"cds_end": null,
"cds_length": 2583,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000519445.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"transcript": "NM_001204824.2",
"protein_id": "NP_001191753.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 752,
"cds_start": 328,
"cds_end": null,
"cds_length": 2259,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001204824.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"transcript": "ENST00000521134.6",
"protein_id": "ENSP00000429799.1",
"transcript_support_level": 2,
"aa_start": 110,
"aa_end": null,
"aa_length": 752,
"cds_start": 328,
"cds_end": null,
"cds_length": 2259,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000521134.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.361C>T",
"hgvs_p": "p.Arg121Cys",
"transcript": "ENST00000638588.1",
"protein_id": "ENSP00000491940.1",
"transcript_support_level": 5,
"aa_start": 121,
"aa_end": null,
"aa_length": 715,
"cds_start": 361,
"cds_end": null,
"cds_length": 2148,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638588.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Arg230Cys",
"transcript": "XM_047421769.1",
"protein_id": "XP_047277725.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 860,
"cds_start": 688,
"cds_end": null,
"cds_length": 2583,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421769.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.466C>T",
"hgvs_p": "p.Arg156Cys",
"transcript": "XM_017013400.2",
"protein_id": "XP_016868889.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 798,
"cds_start": 466,
"cds_end": null,
"cds_length": 2397,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017013400.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"transcript": "XM_011517026.3",
"protein_id": "XP_011515328.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 752,
"cds_start": 328,
"cds_end": null,
"cds_length": 2259,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011517026.3"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "n.466C>T",
"hgvs_p": null,
"transcript": "ENST00000519589.1",
"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": "ENST00000519589.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "n.*69C>T",
"hgvs_p": null,
"transcript": "ENST00000639358.1",
"protein_id": "ENSP00000492691.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000639358.1"
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "n.361C>T",
"hgvs_p": null,
"transcript": "ENST00000639496.1",
"protein_id": "ENSP00000491165.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000639496.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"hgvs_c": "n.*69C>T",
"hgvs_p": null,
"transcript": "ENST00000639358.1",
"protein_id": "ENSP00000492691.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000639358.1"
}
],
"gene_symbol": "KCNQ3",
"gene_hgnc_id": 6297,
"dbsnp": "rs796052676",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9821733236312866,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.96,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9656,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.789,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"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": 22,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 22,
"benign_score": 0,
"pathogenic_score": 22,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_004519.4",
"gene_symbol": "KCNQ3",
"hgnc_id": 6297,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Arg230Cys"
}
],
"clinvar_disease": " 2, 5, benign familial infantile, benign familial neonatal, severe,Benign neonatal seizures,Inborn genetic diseases,Intellectual disability,KCNQ3-related Autism and developmental disability,KCNQ3-related developmental disability,Lennox-Gastaut syndrome,Neurodevelopmental disorder,Seizures,Severe neurodevelopmental delay,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:20 LP:2 O:2",
"phenotype_combined": "not provided|Seizures, benign familial neonatal, 2|Severe neurodevelopmental delay|Seizures, benign familial infantile, 5|Benign neonatal seizures|Intellectual disability|Intellectual disability;Benign neonatal seizures;Lennox-Gastaut syndrome|KCNQ3-related developmental disability|Intellectual disability, severe|Neurodevelopmental disorder|KCNQ3-related Autism and developmental disability|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}