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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: 6-32042485-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=32042485&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 32042485,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000644971.2",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.12180C>G",
"hgvs_p": "p.Cys4060Trp",
"transcript": "NM_001365276.2",
"protein_id": "NP_001352205.1",
"transcript_support_level": null,
"aa_start": 4060,
"aa_end": null,
"aa_length": 4244,
"cds_start": 12180,
"cds_end": null,
"cds_length": 12735,
"cdna_start": 12346,
"cdna_end": null,
"cdna_length": 13097,
"mane_select": "ENST00000644971.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.12180C>G",
"hgvs_p": "p.Cys4060Trp",
"transcript": "ENST00000644971.2",
"protein_id": "ENSP00000496448.1",
"transcript_support_level": null,
"aa_start": 4060,
"aa_end": null,
"aa_length": 4244,
"cds_start": 12180,
"cds_end": null,
"cds_length": 12735,
"cdna_start": 12346,
"cdna_end": null,
"cdna_length": 13097,
"mane_select": "NM_001365276.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.1467C>G",
"hgvs_p": "p.Cys489Trp",
"transcript": "ENST00000451343.4",
"protein_id": "ENSP00000407685.1",
"transcript_support_level": 1,
"aa_start": 489,
"aa_end": null,
"aa_length": 673,
"cds_start": 1467,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 2376,
"cdna_end": null,
"cdna_length": 3125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "n.2007C>G",
"hgvs_p": null,
"transcript": "ENST00000490077.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.12921C>G",
"hgvs_p": "p.Cys4307Trp",
"transcript": "NM_001428335.1",
"protein_id": "NP_001415264.1",
"transcript_support_level": null,
"aa_start": 4307,
"aa_end": null,
"aa_length": 4491,
"cds_start": 12921,
"cds_end": null,
"cds_length": 13476,
"cdna_start": 13087,
"cdna_end": null,
"cdna_length": 13838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.12921C>G",
"hgvs_p": "p.Cys4307Trp",
"transcript": "ENST00000647633.1",
"protein_id": "ENSP00000497649.1",
"transcript_support_level": null,
"aa_start": 4307,
"aa_end": null,
"aa_length": 4491,
"cds_start": 12921,
"cds_end": null,
"cds_length": 13476,
"cdna_start": 13081,
"cdna_end": null,
"cdna_length": 13831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.12180C>G",
"hgvs_p": "p.Cys4060Trp",
"transcript": "ENST00000375244.7",
"protein_id": "ENSP00000364393.3",
"transcript_support_level": 5,
"aa_start": 4060,
"aa_end": null,
"aa_length": 4244,
"cds_start": 12180,
"cds_end": null,
"cds_length": 12735,
"cdna_start": 12382,
"cdna_end": null,
"cdna_length": 13132,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.12174C>G",
"hgvs_p": "p.Cys4058Trp",
"transcript": "NM_019105.8",
"protein_id": "NP_061978.6",
"transcript_support_level": null,
"aa_start": 4058,
"aa_end": null,
"aa_length": 4242,
"cds_start": 12174,
"cds_end": null,
"cds_length": 12729,
"cdna_start": 12340,
"cdna_end": null,
"cdna_length": 13091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "c.1467C>G",
"hgvs_p": "p.Cys489Trp",
"transcript": "NM_032470.4",
"protein_id": "NP_115859.2",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 673,
"cds_start": 1467,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 2376,
"cdna_end": null,
"cdna_length": 3127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"hgvs_c": "n.665C>G",
"hgvs_p": null,
"transcript": "ENST00000498094.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNXB",
"gene_hgnc_id": 11976,
"dbsnp": "rs56345590",
"frequency_reference_population": 0.000032922893,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.0000184826,
"gnomad_genomes_af": 0.0000329229,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8402124643325806,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.551,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9856,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": -0.883,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000644971.2",
"gene_symbol": "TNXB",
"hgnc_id": 11976,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.12180C>G",
"hgvs_p": "p.Cys4060Trp"
}
],
"clinvar_disease": "Ehlers-Danlos syndrome due to tenascin-X deficiency,TNXB-related disorder,Vesicoureteral reflux 8,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:3",
"phenotype_combined": "Ehlers-Danlos syndrome due to tenascin-X deficiency|not provided|Vesicoureteral reflux 8;Ehlers-Danlos syndrome due to tenascin-X deficiency|TNXB-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}