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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: 1-154191927-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=154191927&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 154191927,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000651641.1",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "NM_152263.4",
"protein_id": "NP_689476.2",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 285,
"cds_start": 92,
"cds_end": null,
"cds_length": 858,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 7064,
"mane_select": "ENST00000651641.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "ENST00000651641.1",
"protein_id": "ENSP00000498577.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 285,
"cds_start": 92,
"cds_end": null,
"cds_length": 858,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 7064,
"mane_select": "NM_152263.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "ENST00000368530.7",
"protein_id": "ENSP00000357516.3",
"transcript_support_level": 1,
"aa_start": 31,
"aa_end": null,
"aa_length": 285,
"cds_start": 92,
"cds_end": null,
"cds_length": 858,
"cdna_start": 150,
"cdna_end": null,
"cdna_length": 1111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "NM_001364679.2",
"protein_id": "NP_001351608.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 285,
"cds_start": 92,
"cds_end": null,
"cds_length": 858,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 3271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "NM_001364680.2",
"protein_id": "NP_001351609.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 285,
"cds_start": 92,
"cds_end": null,
"cds_length": 858,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 3271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "NM_001364682.1",
"protein_id": "NP_001351611.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 285,
"cds_start": 92,
"cds_end": null,
"cds_length": 858,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 7064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "ENST00000271850.11",
"protein_id": "ENSP00000271850.7",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 285,
"cds_start": 92,
"cds_end": null,
"cds_length": 858,
"cdna_start": 132,
"cdna_end": null,
"cdna_length": 1219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "NM_001364681.2",
"protein_id": "NP_001351610.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 284,
"cds_start": 92,
"cds_end": null,
"cds_length": 855,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 4598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr",
"transcript": "ENST00000515609.1",
"protein_id": "ENSP00000426306.1",
"transcript_support_level": 3,
"aa_start": 31,
"aa_end": null,
"aa_length": 74,
"cds_start": 92,
"cds_end": null,
"cds_length": 226,
"cdna_start": 453,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "n.22A>C",
"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": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "n.92A>C",
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPM3",
"gene_hgnc_id": 12012,
"hgvs_c": "n.174A>C",
"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": "rs62000429",
"frequency_reference_population": 0.0010168118,
"hom_count_reference_population": 18,
"allele_count_reference_population": 1641,
"gnomad_exomes_af": 0.000552845,
"gnomad_genomes_af": 0.00546818,
"gnomad_exomes_ac": 808,
"gnomad_genomes_ac": 833,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008729010820388794,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.795,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5124,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000651641.1",
"gene_symbol": "TPM3",
"hgnc_id": 12012,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,SD,AR",
"hgvs_c": "c.92A>C",
"hgvs_p": "p.Lys31Thr"
}
],
"clinvar_disease": " autosomal recessive,Congenital myopathy 4B,Congenital myopathy with fiber type disproportion,TPM3-related disorder,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:4",
"phenotype_combined": "not provided|not specified|Congenital myopathy with fiber type disproportion;Congenital myopathy 4B, autosomal recessive|TPM3-related disorder|Congenital myopathy 4B, autosomal recessive|Congenital myopathy with fiber type disproportion",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}