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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: 18-68684474-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=68684474&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 68684474,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_019022.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Ala250Thr",
"transcript": "NM_019022.5",
"protein_id": "NP_061895.3",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 454,
"cds_start": 748,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000299608.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019022.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Ala250Thr",
"transcript": "ENST00000299608.7",
"protein_id": "ENSP00000299608.2",
"transcript_support_level": 1,
"aa_start": 250,
"aa_end": null,
"aa_length": 454,
"cds_start": 748,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_019022.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000299608.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "n.*432G>A",
"hgvs_p": null,
"transcript": "ENST00000564631.5",
"protein_id": "ENSP00000456587.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000564631.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "n.*432G>A",
"hgvs_p": null,
"transcript": "ENST00000564631.5",
"protein_id": "ENSP00000456587.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000564631.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.871G>A",
"hgvs_p": "p.Ala291Thr",
"transcript": "ENST00000915516.1",
"protein_id": "ENSP00000585575.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 495,
"cds_start": 871,
"cds_end": null,
"cds_length": 1488,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915516.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.814G>A",
"hgvs_p": "p.Ala272Thr",
"transcript": "ENST00000903507.1",
"protein_id": "ENSP00000573566.1",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 476,
"cds_start": 814,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903507.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.769G>A",
"hgvs_p": "p.Ala257Thr",
"transcript": "ENST00000961335.1",
"protein_id": "ENSP00000631394.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 461,
"cds_start": 769,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961335.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.724G>A",
"hgvs_p": "p.Ala242Thr",
"transcript": "ENST00000915517.1",
"protein_id": "ENSP00000585576.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 446,
"cds_start": 724,
"cds_end": null,
"cds_length": 1341,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915517.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.667G>A",
"hgvs_p": "p.Ala223Thr",
"transcript": "NM_001350514.2",
"protein_id": "NP_001337443.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 427,
"cds_start": 667,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350514.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.667G>A",
"hgvs_p": "p.Ala223Thr",
"transcript": "ENST00000903506.1",
"protein_id": "ENSP00000573565.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 427,
"cds_start": 667,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903506.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.529G>A",
"hgvs_p": "p.Ala177Thr",
"transcript": "ENST00000961336.1",
"protein_id": "ENSP00000631395.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 381,
"cds_start": 529,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961336.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.325G>A",
"hgvs_p": "p.Ala109Thr",
"transcript": "NM_001350515.2",
"protein_id": "NP_001337444.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 313,
"cds_start": 325,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350515.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.325G>A",
"hgvs_p": "p.Ala109Thr",
"transcript": "NM_001350516.2",
"protein_id": "NP_001337445.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 313,
"cds_start": 325,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350516.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "c.325G>A",
"hgvs_p": "p.Ala109Thr",
"transcript": "NM_001350517.2",
"protein_id": "NP_001337446.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 313,
"cds_start": 325,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350517.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "n.323G>A",
"hgvs_p": null,
"transcript": "ENST00000578765.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000578765.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"hgvs_c": "n.875G>A",
"hgvs_p": null,
"transcript": "XR_935227.3",
"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": "XR_935227.3"
}
],
"gene_symbol": "TMX3",
"gene_hgnc_id": 24718,
"dbsnp": "rs953535128",
"frequency_reference_population": 0.0000024805986,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000136946,
"gnomad_genomes_af": 0.000013151,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4510009288787842,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.077,
"revel_prediction": "Benign",
"alphamissense_score": 0.1361,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.151,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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_019022.5",
"gene_symbol": "TMX3",
"hgnc_id": 24718,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Ala250Thr"
}
],
"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
}