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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: 9-136792016-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136792016&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 136792016,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_032928.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.191T>A",
"hgvs_p": "p.Leu64His",
"transcript": "NM_032928.4",
"protein_id": "NP_116317.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 108,
"cds_start": 191,
"cds_end": null,
"cds_length": 327,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000290079.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032928.4"
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.191T>A",
"hgvs_p": "p.Leu64His",
"transcript": "ENST00000290079.9",
"protein_id": "ENSP00000290079.8",
"transcript_support_level": 1,
"aa_start": 64,
"aa_end": null,
"aa_length": 108,
"cds_start": 191,
"cds_end": null,
"cds_length": 327,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032928.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000290079.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272896",
"gene_hgnc_id": null,
"hgvs_c": "n.115T>A",
"hgvs_p": null,
"transcript": "ENST00000456614.2",
"protein_id": "ENSP00000476927.2",
"transcript_support_level": 4,
"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": "ENST00000456614.2"
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.272T>A",
"hgvs_p": "p.Leu91His",
"transcript": "ENST00000885942.1",
"protein_id": "ENSP00000556001.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 135,
"cds_start": 272,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885942.1"
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.191T>A",
"hgvs_p": "p.Leu64His",
"transcript": "ENST00000929971.1",
"protein_id": "ENSP00000600030.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 106,
"cds_start": 191,
"cds_end": null,
"cds_length": 321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929971.1"
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.146T>A",
"hgvs_p": "p.Leu49His",
"transcript": "ENST00000885943.1",
"protein_id": "ENSP00000556002.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 93,
"cds_start": 146,
"cds_end": null,
"cds_length": 282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885943.1"
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.98T>A",
"hgvs_p": "p.Leu33His",
"transcript": "ENST00000885944.1",
"protein_id": "ENSP00000556003.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 77,
"cds_start": 98,
"cds_end": null,
"cds_length": 234,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885944.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.203-235T>A",
"hgvs_p": null,
"transcript": "ENST00000929972.1",
"protein_id": "ENSP00000600031.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 107,
"cds_start": null,
"cds_end": null,
"cds_length": 324,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929972.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "c.122-235T>A",
"hgvs_p": null,
"transcript": "ENST00000929970.1",
"protein_id": "ENSP00000600029.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": null,
"cds_end": null,
"cds_length": 243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929970.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "n.279T>A",
"hgvs_p": null,
"transcript": "ENST00000465017.5",
"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": "pseudogene",
"feature": "ENST00000465017.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "n.285T>A",
"hgvs_p": null,
"transcript": "ENST00000479737.1",
"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": "ENST00000479737.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "n.123T>A",
"hgvs_p": null,
"transcript": "ENST00000483187.5",
"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": "pseudogene",
"feature": "ENST00000483187.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "n.457T>A",
"hgvs_p": null,
"transcript": "ENST00000484854.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000484854.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"hgvs_c": "n.158T>A",
"hgvs_p": null,
"transcript": "ENST00000489739.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000489739.1"
}
],
"gene_symbol": "TMEM141",
"gene_hgnc_id": 28211,
"dbsnp": "rs749588332",
"frequency_reference_population": 0.0000074357645,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000615739,
"gnomad_genomes_af": 0.0000197156,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.33466076850891113,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.211,
"revel_prediction": "Benign",
"alphamissense_score": 0.5146,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.973,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032928.4",
"gene_symbol": "TMEM141",
"hgnc_id": 28211,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.191T>A",
"hgvs_p": "p.Leu64His"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000456614.2",
"gene_symbol": "ENSG00000272896",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.115T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}