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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: 5-114362492-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=114362492&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 114362492,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001372233.1",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Ser118Leu",
"transcript": "NM_021614.4",
"protein_id": "NP_067627.3",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 791,
"cds_start": 353,
"cds_end": null,
"cds_length": 2376,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000673685.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021614.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Ser118Leu",
"transcript": "ENST00000673685.1",
"protein_id": "ENSP00000501239.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 791,
"cds_start": 353,
"cds_end": null,
"cds_length": 2376,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_021614.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000673685.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "c.551C>T",
"hgvs_p": "p.Ser184Leu",
"transcript": "NM_001372233.1",
"protein_id": "NP_001359162.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 857,
"cds_start": 551,
"cds_end": null,
"cds_length": 2574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001372233.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "c.551C>T",
"hgvs_p": "p.Ser184Leu",
"transcript": "ENST00000512097.10",
"protein_id": "ENSP00000427120.4",
"transcript_support_level": 5,
"aa_start": 184,
"aa_end": null,
"aa_length": 857,
"cds_start": 551,
"cds_end": null,
"cds_length": 2574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512097.10"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "c.551C>T",
"hgvs_p": "p.Ser184Leu",
"transcript": "XM_011543389.2",
"protein_id": "XP_011541691.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 857,
"cds_start": 551,
"cds_end": null,
"cds_length": 2574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543389.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "c.521C>T",
"hgvs_p": "p.Ser174Leu",
"transcript": "XM_047417166.1",
"protein_id": "XP_047273122.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 847,
"cds_start": 521,
"cds_end": null,
"cds_length": 2544,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417166.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "n.423C>T",
"hgvs_p": null,
"transcript": "NR_174097.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_174097.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"hgvs_c": "c.-248C>T",
"hgvs_p": null,
"transcript": "ENST00000631899.2",
"protein_id": "ENSP00000487849.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 594,
"cds_start": null,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000631899.2"
}
],
"gene_symbol": "KCNN2",
"gene_hgnc_id": 6291,
"dbsnp": "rs544525765",
"frequency_reference_population": 0.00033046643,
"hom_count_reference_population": 1,
"allele_count_reference_population": 154,
"gnomad_exomes_af": 0.000372657,
"gnomad_genomes_af": 0.000243347,
"gnomad_exomes_ac": 117,
"gnomad_genomes_ac": 37,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23983022570610046,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.5112,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.872,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 6,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001372233.1",
"gene_symbol": "KCNN2",
"hgnc_id": 6291,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.551C>T",
"hgvs_p": "p.Ser184Leu"
}
],
"clinvar_disease": "Neurodevelopmental disorder with or without variable movement or behavioral abnormalities",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Neurodevelopmental disorder with or without variable movement or behavioral abnormalities",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}