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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: 20-49373036-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=49373036&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 49373036,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_004975.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"hgvs_c": "c.2524C>T",
"hgvs_p": "p.Arg842Cys",
"transcript": "NM_004975.4",
"protein_id": "NP_004966.1",
"transcript_support_level": null,
"aa_start": 842,
"aa_end": null,
"aa_length": 858,
"cds_start": 2524,
"cds_end": null,
"cds_length": 2577,
"cdna_start": 2712,
"cdna_end": null,
"cdna_length": 11871,
"mane_select": "ENST00000371741.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"hgvs_c": "c.2524C>T",
"hgvs_p": "p.Arg842Cys",
"transcript": "ENST00000371741.6",
"protein_id": "ENSP00000360806.3",
"transcript_support_level": 1,
"aa_start": 842,
"aa_end": null,
"aa_length": 858,
"cds_start": 2524,
"cds_end": null,
"cds_length": 2577,
"cdna_start": 2712,
"cdna_end": null,
"cdna_length": 11871,
"mane_select": "NM_004975.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"hgvs_c": "c.2524C>T",
"hgvs_p": "p.Arg842Cys",
"transcript": "ENST00000635465.1",
"protein_id": "ENSP00000489193.1",
"transcript_support_level": 1,
"aa_start": 842,
"aa_end": null,
"aa_length": 858,
"cds_start": 2524,
"cds_end": null,
"cds_length": 2577,
"cdna_start": 3046,
"cdna_end": null,
"cdna_length": 4114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"hgvs_c": "c.2524C>T",
"hgvs_p": "p.Arg842Cys",
"transcript": "XM_011528799.3",
"protein_id": "XP_011527101.1",
"transcript_support_level": null,
"aa_start": 842,
"aa_end": null,
"aa_length": 858,
"cds_start": 2524,
"cds_end": null,
"cds_length": 2577,
"cdna_start": 2812,
"cdna_end": null,
"cdna_length": 11971,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"hgvs_c": "n.67C>T",
"hgvs_p": null,
"transcript": "ENST00000637131.1",
"protein_id": "ENSP00000489766.1",
"transcript_support_level": 5,
"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": 1050,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"hgvs_c": "c.97-73653C>T",
"hgvs_p": null,
"transcript": "ENST00000635878.1",
"protein_id": "ENSP00000489908.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 42,
"cds_start": -4,
"cds_end": null,
"cds_length": 129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290421",
"gene_hgnc_id": null,
"hgvs_c": "n.206+41012G>A",
"hgvs_p": null,
"transcript": "ENST00000637341.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 1688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC105372649",
"gene_hgnc_id": null,
"hgvs_c": "n.1201+41012G>A",
"hgvs_p": null,
"transcript": "XR_001754659.2",
"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": 1750,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"hgvs_c": "n.-86C>T",
"hgvs_p": null,
"transcript": "ENST00000636838.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 5331,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KCNB1",
"gene_hgnc_id": 6231,
"dbsnp": "rs758964585",
"frequency_reference_population": 0.000017969474,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000164186,
"gnomad_genomes_af": 0.0000328757,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.34654223918914795,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.427,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.416,
"phylop100way_prediction": "Uncertain_significance",
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004975.4",
"gene_symbol": "KCNB1",
"hgnc_id": 6231,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2524C>T",
"hgvs_p": "p.Arg842Cys"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "XR_001754659.2",
"gene_symbol": "LOC105372649",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1201+41012G>A",
"hgvs_p": null
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000637341.1",
"gene_symbol": "ENSG00000290421",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.206+41012G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 26,Developmental and epileptic encephalopathy,Inborn genetic diseases",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Developmental and epileptic encephalopathy, 26|Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}