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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: 19-2416798-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=2416798&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 2416798,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000696167.1",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.2006A>G",
"hgvs_p": "p.Gln669Arg",
"transcript": "NM_001395513.1",
"protein_id": "NP_001382442.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1093,
"cds_start": 2006,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 2127,
"cdna_end": null,
"cdna_length": 3576,
"mane_select": "ENST00000696167.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.2006A>G",
"hgvs_p": "p.Gln669Arg",
"transcript": "ENST00000696167.1",
"protein_id": "ENSP00000512457.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1093,
"cds_start": 2006,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 2127,
"cdna_end": null,
"cdna_length": 3576,
"mane_select": "NM_001395513.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.2006A>G",
"hgvs_p": "p.Gln669Arg",
"transcript": "ENST00000648592.1",
"protein_id": "ENSP00000498031.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1093,
"cds_start": 2006,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 2031,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.1904A>G",
"hgvs_p": "p.Gln635Arg",
"transcript": "NM_182973.3",
"protein_id": "NP_892018.1",
"transcript_support_level": null,
"aa_start": 635,
"aa_end": null,
"aa_length": 1059,
"cds_start": 1904,
"cds_end": null,
"cds_length": 3180,
"cdna_start": 2154,
"cdna_end": null,
"cdna_length": 3603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.1904A>G",
"hgvs_p": "p.Gln635Arg",
"transcript": "ENST00000649857.1",
"protein_id": "ENSP00000497651.1",
"transcript_support_level": null,
"aa_start": 635,
"aa_end": null,
"aa_length": 1059,
"cds_start": 1904,
"cds_end": null,
"cds_length": 3180,
"cdna_start": 2052,
"cdna_end": null,
"cdna_length": 3479,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.1310A>G",
"hgvs_p": "p.Gln437Arg",
"transcript": "NM_001385642.1",
"protein_id": "NP_001372571.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 861,
"cds_start": 1310,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2115,
"cdna_end": null,
"cdna_length": 3564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.2006A>G",
"hgvs_p": "p.Gln669Arg",
"transcript": "XM_011527978.3",
"protein_id": "XP_011526280.1",
"transcript_support_level": null,
"aa_start": 669,
"aa_end": null,
"aa_length": 1093,
"cds_start": 2006,
"cds_end": null,
"cds_length": 3282,
"cdna_start": 2265,
"cdna_end": null,
"cdna_length": 3714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.1973A>G",
"hgvs_p": "p.Gln658Arg",
"transcript": "XM_047438776.1",
"protein_id": "XP_047294732.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 1082,
"cds_start": 1973,
"cds_end": null,
"cds_length": 3249,
"cdna_start": 1995,
"cdna_end": null,
"cdna_length": 3444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.1310A>G",
"hgvs_p": "p.Gln437Arg",
"transcript": "XM_047438777.1",
"protein_id": "XP_047294733.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 861,
"cds_start": 1310,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2111,
"cdna_end": null,
"cdna_length": 3560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "c.797A>G",
"hgvs_p": "p.Gln266Arg",
"transcript": "XM_011527980.1",
"protein_id": "XP_011526282.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 690,
"cds_start": 797,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 923,
"cdna_end": null,
"cdna_length": 2372,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"hgvs_c": "n.556A>G",
"hgvs_p": null,
"transcript": "ENST00000587863.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124904612",
"gene_hgnc_id": null,
"hgvs_c": "n.*27T>C",
"hgvs_p": null,
"transcript": "XR_007067089.1",
"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": 432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMPRSS9",
"gene_hgnc_id": 30079,
"dbsnp": "rs45546534",
"frequency_reference_population": 0.044701636,
"hom_count_reference_population": 1874,
"allele_count_reference_population": 71937,
"gnomad_exomes_af": 0.0448411,
"gnomad_genomes_af": 0.0433666,
"gnomad_exomes_ac": 65334,
"gnomad_genomes_ac": 6603,
"gnomad_exomes_homalt": 1705,
"gnomad_genomes_homalt": 169,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0025051236152648926,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.213,
"revel_prediction": "Benign",
"alphamissense_score": 0.0635,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.562,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000696167.1",
"gene_symbol": "TMPRSS9",
"hgnc_id": 30079,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2006A>G",
"hgvs_p": "p.Gln669Arg"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007067089.1",
"gene_symbol": "LOC124904612",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*27T>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}