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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: 4-121879822-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=121879822&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 121879822,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001130698.2",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2680G>A",
"hgvs_p": "p.Asp894Asn",
"transcript": "NM_001130698.2",
"protein_id": "NP_001124170.1",
"transcript_support_level": null,
"aa_start": 894,
"aa_end": null,
"aa_length": 921,
"cds_start": 2680,
"cds_end": null,
"cds_length": 2766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379645.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130698.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2680G>A",
"hgvs_p": "p.Asp894Asn",
"transcript": "ENST00000379645.8",
"protein_id": "ENSP00000368966.3",
"transcript_support_level": 1,
"aa_start": 894,
"aa_end": null,
"aa_length": 921,
"cds_start": 2680,
"cds_end": null,
"cds_length": 2766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001130698.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379645.8"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2461G>A",
"hgvs_p": "p.Asp821Asn",
"transcript": "ENST00000264811.9",
"protein_id": "ENSP00000264811.5",
"transcript_support_level": 1,
"aa_start": 821,
"aa_end": null,
"aa_length": 848,
"cds_start": 2461,
"cds_end": null,
"cds_length": 2547,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264811.9"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2296G>A",
"hgvs_p": "p.Asp766Asn",
"transcript": "ENST00000513531.1",
"protein_id": "ENSP00000426899.1",
"transcript_support_level": 1,
"aa_start": 766,
"aa_end": null,
"aa_length": 793,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2382,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513531.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "n.*1688G>A",
"hgvs_p": null,
"transcript": "ENST00000506449.1",
"protein_id": "ENSP00000423866.1",
"transcript_support_level": 1,
"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": "ENST00000506449.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "n.*1688G>A",
"hgvs_p": null,
"transcript": "ENST00000506449.1",
"protein_id": "ENSP00000423866.1",
"transcript_support_level": 1,
"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": "ENST00000506449.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2728G>A",
"hgvs_p": "p.Asp910Asn",
"transcript": "ENST00000949674.1",
"protein_id": "ENSP00000619733.1",
"transcript_support_level": null,
"aa_start": 910,
"aa_end": null,
"aa_length": 937,
"cds_start": 2728,
"cds_end": null,
"cds_length": 2814,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949674.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2677G>A",
"hgvs_p": "p.Asp893Asn",
"transcript": "ENST00000871535.1",
"protein_id": "ENSP00000541594.1",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 920,
"cds_start": 2677,
"cds_end": null,
"cds_length": 2763,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871535.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2596G>A",
"hgvs_p": "p.Asp866Asn",
"transcript": "NM_001366479.2",
"protein_id": "NP_001353408.1",
"transcript_support_level": null,
"aa_start": 866,
"aa_end": null,
"aa_length": 893,
"cds_start": 2596,
"cds_end": null,
"cds_length": 2682,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001366479.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2461G>A",
"hgvs_p": "p.Asp821Asn",
"transcript": "NM_003305.2",
"protein_id": "NP_003296.1",
"transcript_support_level": null,
"aa_start": 821,
"aa_end": null,
"aa_length": 848,
"cds_start": 2461,
"cds_end": null,
"cds_length": 2547,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003305.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2728G>A",
"hgvs_p": "p.Asp910Asn",
"transcript": "XM_011532217.4",
"protein_id": "XP_011530519.1",
"transcript_support_level": null,
"aa_start": 910,
"aa_end": null,
"aa_length": 937,
"cds_start": 2728,
"cds_end": null,
"cds_length": 2814,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532217.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2725G>A",
"hgvs_p": "p.Asp909Asn",
"transcript": "XM_017008578.3",
"protein_id": "XP_016864067.1",
"transcript_support_level": null,
"aa_start": 909,
"aa_end": null,
"aa_length": 936,
"cds_start": 2725,
"cds_end": null,
"cds_length": 2811,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008578.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"hgvs_c": "c.2677G>A",
"hgvs_p": "p.Asp893Asn",
"transcript": "XM_011532218.4",
"protein_id": "XP_011530520.1",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 920,
"cds_start": 2677,
"cds_end": null,
"cds_length": 2763,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532218.4"
}
],
"gene_symbol": "TRPC3",
"gene_hgnc_id": 12335,
"dbsnp": "rs200301137",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3406575918197632,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.322,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.559,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.01,
"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": 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_001130698.2",
"gene_symbol": "TRPC3",
"hgnc_id": 12335,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2680G>A",
"hgvs_p": "p.Asp894Asn"
}
],
"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
}