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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: 13-99554368-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=99554368&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 99554368,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004800.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Thr518Met",
"transcript": "NM_004800.3",
"protein_id": "NP_004791.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 663,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000376387.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004800.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Thr518Met",
"transcript": "ENST00000376387.5",
"protein_id": "ENSP00000365567.3",
"transcript_support_level": 1,
"aa_start": 518,
"aa_end": null,
"aa_length": 663,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004800.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376387.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1655C>T",
"hgvs_p": "p.Thr552Met",
"transcript": "ENST00000865265.1",
"protein_id": "ENSP00000535324.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 697,
"cds_start": 1655,
"cds_end": null,
"cds_length": 2094,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865265.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Thr518Met",
"transcript": "ENST00000642475.1",
"protein_id": "ENSP00000493515.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 663,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000642475.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1514C>T",
"hgvs_p": "p.Thr505Met",
"transcript": "ENST00000951402.1",
"protein_id": "ENSP00000621461.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 650,
"cds_start": 1514,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951402.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1433C>T",
"hgvs_p": "p.Thr478Met",
"transcript": "ENST00000865266.1",
"protein_id": "ENSP00000535325.1",
"transcript_support_level": null,
"aa_start": 478,
"aa_end": null,
"aa_length": 623,
"cds_start": 1433,
"cds_end": null,
"cds_length": 1872,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865266.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1361C>T",
"hgvs_p": "p.Thr454Met",
"transcript": "ENST00000951401.1",
"protein_id": "ENSP00000621460.1",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 599,
"cds_start": 1361,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951401.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1316C>T",
"hgvs_p": "p.Thr439Met",
"transcript": "ENST00000930902.1",
"protein_id": "ENSP00000600961.1",
"transcript_support_level": null,
"aa_start": 439,
"aa_end": null,
"aa_length": 584,
"cds_start": 1316,
"cds_end": null,
"cds_length": 1755,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930902.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1298C>T",
"hgvs_p": "p.Thr433Met",
"transcript": "ENST00000865264.1",
"protein_id": "ENSP00000535323.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 578,
"cds_start": 1298,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865264.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1196C>T",
"hgvs_p": "p.Thr399Met",
"transcript": "ENST00000951399.1",
"protein_id": "ENSP00000621458.1",
"transcript_support_level": null,
"aa_start": 399,
"aa_end": null,
"aa_length": 544,
"cds_start": 1196,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951399.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Thr518Met",
"transcript": "ENST00000951404.1",
"protein_id": "ENSP00000621463.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 544,
"cds_start": 1553,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951404.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1058C>T",
"hgvs_p": "p.Thr353Met",
"transcript": "ENST00000865267.1",
"protein_id": "ENSP00000535326.1",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 498,
"cds_start": 1058,
"cds_end": null,
"cds_length": 1497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865267.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.869C>T",
"hgvs_p": "p.Thr290Met",
"transcript": "ENST00000951403.1",
"protein_id": "ENSP00000621462.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 435,
"cds_start": 869,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951403.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.398C>T",
"hgvs_p": "p.Thr133Met",
"transcript": "ENST00000951400.1",
"protein_id": "ENSP00000621459.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 278,
"cds_start": 398,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951400.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1488+2042C>T",
"hgvs_p": null,
"transcript": "ENST00000930903.1",
"protein_id": "ENSP00000600962.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 575,
"cds_start": null,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930903.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"hgvs_c": "c.1329-1168C>T",
"hgvs_p": null,
"transcript": "ENST00000951398.1",
"protein_id": "ENSP00000621457.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 559,
"cds_start": null,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951398.1"
}
],
"gene_symbol": "TM9SF2",
"gene_hgnc_id": 11865,
"dbsnp": "rs370181033",
"frequency_reference_population": 0.000024782134,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.0000259947,
"gnomad_genomes_af": 0.0000131382,
"gnomad_exomes_ac": 38,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.44873374700546265,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.315,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6742,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.705,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004800.3",
"gene_symbol": "TM9SF2",
"hgnc_id": 11865,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1553C>T",
"hgvs_p": "p.Thr518Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}