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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: 1-154191285-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=154191285&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 154191285,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000651641.1",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "NM_152263.4",
"protein_id": "NP_689476.2",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 285,
"cds_start": 144,
"cds_end": null,
"cds_length": 858,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 7064,
"mane_select": "ENST00000651641.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "ENST00000651641.1",
"protein_id": "ENSP00000498577.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 285,
"cds_start": 144,
"cds_end": null,
"cds_length": 858,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 7064,
"mane_select": "NM_152263.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "ENST00000368530.7",
"protein_id": "ENSP00000357516.3",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 285,
"cds_start": 144,
"cds_end": null,
"cds_length": 858,
"cdna_start": 202,
"cdna_end": null,
"cdna_length": 1111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "NM_001364679.2",
"protein_id": "NP_001351608.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 285,
"cds_start": 144,
"cds_end": null,
"cds_length": 858,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 3271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "NM_001364680.2",
"protein_id": "NP_001351609.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 285,
"cds_start": 144,
"cds_end": null,
"cds_length": 858,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 3271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "NM_001364682.1",
"protein_id": "NP_001351611.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 285,
"cds_start": 144,
"cds_end": null,
"cds_length": 858,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 7064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "ENST00000271850.11",
"protein_id": "ENSP00000271850.7",
"transcript_support_level": 5,
"aa_start": 48,
"aa_end": null,
"aa_length": 285,
"cds_start": 144,
"cds_end": null,
"cds_length": 858,
"cdna_start": 184,
"cdna_end": null,
"cdna_length": 1219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "NM_001364681.2",
"protein_id": "NP_001351610.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 284,
"cds_start": 144,
"cds_end": null,
"cds_length": 855,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 4598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln",
"transcript": "ENST00000515609.1",
"protein_id": "ENSP00000426306.1",
"transcript_support_level": 3,
"aa_start": 48,
"aa_end": null,
"aa_length": 74,
"cds_start": 144,
"cds_end": null,
"cds_length": 226,
"cdna_start": 505,
"cdna_end": null,
"cdna_length": 587,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "n.179G>A",
"hgvs_p": null,
"transcript": "ENST00000466010.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 461,
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "n.144G>A",
"hgvs_p": null,
"transcript": "ENST00000651644.1",
"protein_id": "ENSP00000498648.1",
"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": 810,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "n.331G>A",
"hgvs_p": null,
"transcript": "NR_103460.2",
"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": 615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"dbsnp": "rs765923858",
"frequency_reference_population": 0.000027880315,
"hom_count_reference_population": 0,
"allele_count_reference_population": 45,
"gnomad_exomes_af": 0.0000253107,
"gnomad_genomes_af": 0.000052559,
"gnomad_exomes_ac": 37,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3199999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.277,
"phylop100way_prediction": "Benign",
"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": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000651641.1",
"gene_symbol": "TPM3",
"hgnc_id": 12012,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,SD,AR",
"hgvs_c": "c.144G>A",
"hgvs_p": "p.Gln48Gln"
}
],
"clinvar_disease": " autosomal recessive,Congenital myopathy 4B,Congenital myopathy with fiber type disproportion",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Congenital myopathy with fiber type disproportion;Congenital myopathy 4B, autosomal recessive",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}