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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: 21-42376577-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=42376577&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 42376577,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000644384.2",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "c.1155C>T",
"hgvs_p": "p.Cys385Cys",
"transcript": "NM_001256317.3",
"protein_id": "NP_001243246.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 453,
"cds_start": 1155,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 1317,
"cdna_end": null,
"cdna_length": 2396,
"mane_select": "ENST00000644384.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "c.1155C>T",
"hgvs_p": "p.Cys385Cys",
"transcript": "ENST00000644384.2",
"protein_id": "ENSP00000494414.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 453,
"cds_start": 1155,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 1317,
"cdna_end": null,
"cdna_length": 2396,
"mane_select": "NM_001256317.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "c.1158C>T",
"hgvs_p": "p.Cys386Cys",
"transcript": "ENST00000433957.7",
"protein_id": "ENSP00000411013.3",
"transcript_support_level": 1,
"aa_start": 386,
"aa_end": null,
"aa_length": 454,
"cds_start": 1158,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1320,
"cdna_end": null,
"cdna_length": 2402,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "n.1026C>T",
"hgvs_p": null,
"transcript": "ENST00000474596.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2105,
"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": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "n.1445C>T",
"hgvs_p": null,
"transcript": "ENST00000482761.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 2524,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "c.1158C>T",
"hgvs_p": "p.Cys386Cys",
"transcript": "NM_024022.4",
"protein_id": "NP_076927.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 454,
"cds_start": 1158,
"cds_end": null,
"cds_length": 1365,
"cdna_start": 1320,
"cdna_end": null,
"cdna_length": 2399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "c.1155C>T",
"hgvs_p": "p.Cys385Cys",
"transcript": "ENST00000652415.1",
"protein_id": "ENSP00000498756.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 453,
"cds_start": 1155,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 1507,
"cdna_end": null,
"cdna_length": 2544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.Cys383Cys",
"transcript": "ENST00000398405.5",
"protein_id": "ENSP00000381442.1",
"transcript_support_level": 5,
"aa_start": 383,
"aa_end": null,
"aa_length": 451,
"cds_start": 1149,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1675,
"cdna_end": null,
"cdna_length": 2754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "c.777C>T",
"hgvs_p": "p.Cys259Cys",
"transcript": "NM_032404.3",
"protein_id": "NP_115780.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 327,
"cds_start": 777,
"cds_end": null,
"cds_length": 984,
"cdna_start": 1057,
"cdna_end": null,
"cdna_length": 2136,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"hgvs_c": "n.1890C>T",
"hgvs_p": null,
"transcript": "ENST00000476848.5",
"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": 2969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMPRSS3",
"gene_hgnc_id": 11877,
"dbsnp": "rs746293388",
"frequency_reference_population": 0.00013819156,
"hom_count_reference_population": 0,
"allele_count_reference_population": 223,
"gnomad_exomes_af": 0.000145056,
"gnomad_genomes_af": 0.0000722724,
"gnomad_exomes_ac": 212,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5099999904632568,
"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": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.163,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000644384.2",
"gene_symbol": "TMPRSS3",
"hgnc_id": 11877,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1155C>T",
"hgvs_p": "p.Cys385Cys"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}