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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: 6-32097988-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=32097988&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 32097988,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001428335.1",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu",
"transcript": "NM_001365276.2",
"protein_id": "NP_001352205.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 4244,
"cds_start": 211,
"cds_end": null,
"cds_length": 12735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000644971.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365276.2"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu",
"transcript": "ENST00000644971.2",
"protein_id": "ENSP00000496448.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 4244,
"cds_start": 211,
"cds_end": null,
"cds_length": 12735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001365276.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644971.2"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu",
"transcript": "ENST00000479795.1",
"protein_id": "ENSP00000418248.1",
"transcript_support_level": 1,
"aa_start": 71,
"aa_end": null,
"aa_length": 842,
"cds_start": 211,
"cds_end": null,
"cds_length": 2529,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000479795.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "n.260G>T",
"hgvs_p": null,
"transcript": "ENST00000486148.1",
"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": "ENST00000486148.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu",
"transcript": "NM_001428335.1",
"protein_id": "NP_001415264.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 4491,
"cds_start": 211,
"cds_end": null,
"cds_length": 13476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001428335.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu",
"transcript": "ENST00000647633.1",
"protein_id": "ENSP00000497649.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 4491,
"cds_start": 211,
"cds_end": null,
"cds_length": 13476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647633.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu",
"transcript": "ENST00000375244.7",
"protein_id": "ENSP00000364393.3",
"transcript_support_level": 5,
"aa_start": 71,
"aa_end": null,
"aa_length": 4244,
"cds_start": 211,
"cds_end": null,
"cds_length": 12735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375244.7"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu",
"transcript": "NM_019105.8",
"protein_id": "NP_061978.6",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 4242,
"cds_start": 211,
"cds_end": null,
"cds_length": 12729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019105.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.*188G>T",
"hgvs_p": null,
"transcript": "ENST00000442721.1",
"protein_id": "ENSP00000389946.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 6,
"cds_start": null,
"cds_end": null,
"cds_length": 23,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442721.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284829",
"gene_hgnc_id": null,
"hgvs_c": "n.*188G>T",
"hgvs_p": null,
"transcript": "ENST00000494022.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000494022.1"
}
],
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"dbsnp": "rs201922477",
"frequency_reference_population": 0.00029927713,
"hom_count_reference_population": 1,
"allele_count_reference_population": 481,
"gnomad_exomes_af": 0.000300343,
"gnomad_genomes_af": 0.000289086,
"gnomad_exomes_ac": 437,
"gnomad_genomes_ac": 44,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.25198662281036377,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.352,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7681,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.123,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001428335.1",
"gene_symbol": "TNXB",
"hgnc_id": 11976,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.211G>T",
"hgvs_p": "p.Val71Leu"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000494022.1",
"gene_symbol": "ENSG00000284829",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*188G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Cardiovascular phenotype,Ehlers-Danlos syndrome due to tenascin-X deficiency,TNXB-related disorder,Vesicoureteral reflux 8,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:7",
"phenotype_combined": "not provided|TNXB-related disorder|Ehlers-Danlos syndrome due to tenascin-X deficiency|Cardiovascular phenotype|Vesicoureteral reflux 8;Ehlers-Danlos syndrome due to tenascin-X deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}