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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: 19-2402007-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=2402007&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 2402007,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001395513.1",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.547T>C",
"hgvs_p": "p.Phe183Leu",
"transcript": "NM_001395513.1",
"protein_id": "NP_001382442.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1093,
"cds_start": 547,
"cds_end": null,
"cds_length": 3282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000696167.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001395513.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.547T>C",
"hgvs_p": "p.Phe183Leu",
"transcript": "ENST00000696167.1",
"protein_id": "ENSP00000512457.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1093,
"cds_start": 547,
"cds_end": null,
"cds_length": 3282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001395513.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696167.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "n.562T>C",
"hgvs_p": null,
"transcript": "ENST00000395264.3",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000395264.3"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.547T>C",
"hgvs_p": "p.Phe183Leu",
"transcript": "ENST00000648592.1",
"protein_id": "ENSP00000498031.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1093,
"cds_start": 547,
"cds_end": null,
"cds_length": 3282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648592.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.445T>C",
"hgvs_p": "p.Phe149Leu",
"transcript": "NM_182973.3",
"protein_id": "NP_892018.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 1059,
"cds_start": 445,
"cds_end": null,
"cds_length": 3180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_182973.3"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.445T>C",
"hgvs_p": "p.Phe149Leu",
"transcript": "ENST00000649857.1",
"protein_id": "ENSP00000497651.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 1059,
"cds_start": 445,
"cds_end": null,
"cds_length": 3180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649857.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.547T>C",
"hgvs_p": "p.Phe183Leu",
"transcript": "XM_011527978.3",
"protein_id": "XP_011526280.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1093,
"cds_start": 547,
"cds_end": null,
"cds_length": 3282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527978.3"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.514T>C",
"hgvs_p": "p.Phe172Leu",
"transcript": "XM_047438776.1",
"protein_id": "XP_047294732.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 1082,
"cds_start": 514,
"cds_end": null,
"cds_length": 3249,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438776.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.-150T>C",
"hgvs_p": null,
"transcript": "NM_001385642.1",
"protein_id": "NP_001372571.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 861,
"cds_start": null,
"cds_end": null,
"cds_length": 2586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001385642.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.-150T>C",
"hgvs_p": null,
"transcript": "XM_047438777.1",
"protein_id": "XP_047294733.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 861,
"cds_start": null,
"cds_end": null,
"cds_length": 2586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438777.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "n.656T>C",
"hgvs_p": null,
"transcript": "NR_169739.1",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_169739.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "n.652T>C",
"hgvs_p": null,
"transcript": "NR_169740.1",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_169740.1"
}
],
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"dbsnp": "rs777724935",
"frequency_reference_population": 0.000013704957,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.000013705,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.025367647409439087,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.166,
"revel_prediction": "Benign",
"alphamissense_score": 0.119,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.177,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001395513.1",
"gene_symbol": "TMPRSS9",
"hgnc_id": 30079,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.547T>C",
"hgvs_p": "p.Phe183Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}