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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: 7-150947854-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=150947854&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 150947854,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000262186.10",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2717C>T",
"hgvs_p": "p.Ser906Leu",
"transcript": "NM_000238.4",
"protein_id": "NP_000229.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 1159,
"cds_start": 2717,
"cds_end": null,
"cds_length": 3480,
"cdna_start": 3125,
"cdna_end": null,
"cdna_length": 4292,
"mane_select": "ENST00000262186.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2717C>T",
"hgvs_p": "p.Ser906Leu",
"transcript": "ENST00000262186.10",
"protein_id": "ENSP00000262186.5",
"transcript_support_level": 1,
"aa_start": 906,
"aa_end": null,
"aa_length": 1159,
"cds_start": 2717,
"cds_end": null,
"cds_length": 3480,
"cdna_start": 3125,
"cdna_end": null,
"cdna_length": 4292,
"mane_select": "NM_000238.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.1697C>T",
"hgvs_p": "p.Ser566Leu",
"transcript": "ENST00000330883.9",
"protein_id": "ENSP00000328531.4",
"transcript_support_level": 1,
"aa_start": 566,
"aa_end": null,
"aa_length": 819,
"cds_start": 1697,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 1998,
"cdna_end": null,
"cdna_length": 3165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2651C>T",
"hgvs_p": "p.Ser884Leu",
"transcript": "ENST00000713710.1",
"protein_id": "ENSP00000519013.1",
"transcript_support_level": null,
"aa_start": 884,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2651,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 2994,
"cdna_end": null,
"cdna_length": 4161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2429C>T",
"hgvs_p": "p.Ser810Leu",
"transcript": "NM_001406753.1",
"protein_id": "NP_001393682.1",
"transcript_support_level": null,
"aa_start": 810,
"aa_end": null,
"aa_length": 1063,
"cds_start": 2429,
"cds_end": null,
"cds_length": 3192,
"cdna_start": 2730,
"cdna_end": null,
"cdna_length": 3897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2417C>T",
"hgvs_p": "p.Ser806Leu",
"transcript": "ENST00000713701.1",
"protein_id": "ENSP00000519004.1",
"transcript_support_level": null,
"aa_start": 806,
"aa_end": null,
"aa_length": 1059,
"cds_start": 2417,
"cds_end": null,
"cds_length": 3180,
"cdna_start": 2582,
"cdna_end": null,
"cdna_length": 3749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.1697C>T",
"hgvs_p": "p.Ser566Leu",
"transcript": "NM_172057.3",
"protein_id": "NP_742054.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 819,
"cds_start": 1697,
"cds_end": null,
"cds_length": 2460,
"cdna_start": 1998,
"cdna_end": null,
"cdna_length": 3165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2795C>T",
"hgvs_p": "p.Ser932Leu",
"transcript": "XM_047420348.1",
"protein_id": "XP_047276304.1",
"transcript_support_level": null,
"aa_start": 932,
"aa_end": null,
"aa_length": 1185,
"cds_start": 2795,
"cds_end": null,
"cds_length": 3558,
"cdna_start": 2810,
"cdna_end": null,
"cdna_length": 3977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2567C>T",
"hgvs_p": "p.Ser856Leu",
"transcript": "XM_017012195.2",
"protein_id": "XP_016867684.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 1109,
"cds_start": 2567,
"cds_end": null,
"cds_length": 3330,
"cdna_start": 3199,
"cdna_end": null,
"cdna_length": 4366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2540C>T",
"hgvs_p": "p.Ser847Leu",
"transcript": "XM_017012196.2",
"protein_id": "XP_016867685.1",
"transcript_support_level": null,
"aa_start": 847,
"aa_end": null,
"aa_length": 1100,
"cds_start": 2540,
"cds_end": null,
"cds_length": 3303,
"cdna_start": 2658,
"cdna_end": null,
"cdna_length": 3825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2417C>T",
"hgvs_p": "p.Ser806Leu",
"transcript": "XM_011516185.3",
"protein_id": "XP_011514487.1",
"transcript_support_level": null,
"aa_start": 806,
"aa_end": null,
"aa_length": 1059,
"cds_start": 2417,
"cds_end": null,
"cds_length": 3180,
"cdna_start": 2432,
"cdna_end": null,
"cdna_length": 3599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "n.3550C>T",
"hgvs_p": null,
"transcript": "ENST00000684241.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "n.3101-163C>T",
"hgvs_p": null,
"transcript": "NR_176254.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "n.1974-163C>T",
"hgvs_p": null,
"transcript": "NR_176255.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2978,
"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": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"hgvs_c": "c.2771-163C>T",
"hgvs_p": null,
"transcript": "XM_047420349.1",
"protein_id": "XP_047276305.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 936,
"cds_start": -4,
"cds_end": null,
"cds_length": 2811,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KCNH2",
"gene_hgnc_id": 6251,
"dbsnp": "rs199473435",
"frequency_reference_population": 0.00007919128,
"hom_count_reference_population": 0,
"allele_count_reference_population": 121,
"gnomad_exomes_af": 0.0000835887,
"gnomad_genomes_af": 0.0000394317,
"gnomad_exomes_ac": 115,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8530240654945374,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "CardioboostArm",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.758,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.0803,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.466,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,PP5,BS2_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PP2",
"PP5",
"BS2_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000262186.10",
"gene_symbol": "KCNH2",
"hgnc_id": 6251,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2717C>T",
"hgvs_p": "p.Ser906Leu"
}
],
"clinvar_disease": "Cardiac arrhythmia,Cardiovascular phenotype,Congenital long QT syndrome,KCNH2-related disorder,Long QT syndrome,Long QT syndrome 2,Short QT syndrome type 1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 LP:5 US:4 O:1",
"phenotype_combined": "Congenital long QT syndrome|Long QT syndrome|Long QT syndrome 2|Long QT syndrome 2;Short QT syndrome type 1|Cardiovascular phenotype|not provided|Cardiac arrhythmia|KCNH2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}