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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: 9-114307746-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=114307746&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 114307746,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_032888.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.5185C>A",
"hgvs_p": "p.Gln1729Lys",
"transcript": "NM_032888.4",
"protein_id": "NP_116277.2",
"transcript_support_level": null,
"aa_start": 1729,
"aa_end": null,
"aa_length": 1860,
"cds_start": 5185,
"cds_end": null,
"cds_length": 5583,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000356083.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032888.4"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.5185C>A",
"hgvs_p": "p.Gln1729Lys",
"transcript": "ENST00000356083.8",
"protein_id": "ENSP00000348385.3",
"transcript_support_level": 1,
"aa_start": 1729,
"aa_end": null,
"aa_length": 1860,
"cds_start": 5185,
"cds_end": null,
"cds_length": 5583,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032888.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000356083.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "n.*2622C>A",
"hgvs_p": null,
"transcript": "ENST00000494090.6",
"protein_id": "ENSP00000432928.1",
"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": "ENST00000494090.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "n.*2622C>A",
"hgvs_p": null,
"transcript": "ENST00000494090.6",
"protein_id": "ENSP00000432928.1",
"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": "ENST00000494090.6"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.5179C>A",
"hgvs_p": "p.Gln1727Lys",
"transcript": "XM_011519138.3",
"protein_id": "XP_011517440.1",
"transcript_support_level": null,
"aa_start": 1727,
"aa_end": null,
"aa_length": 1858,
"cds_start": 5179,
"cds_end": null,
"cds_length": 5577,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011519138.3"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.5131C>A",
"hgvs_p": "p.Gln1711Lys",
"transcript": "XM_006717308.3",
"protein_id": "XP_006717371.1",
"transcript_support_level": null,
"aa_start": 1711,
"aa_end": null,
"aa_length": 1842,
"cds_start": 5131,
"cds_end": null,
"cds_length": 5529,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717308.3"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.5131C>A",
"hgvs_p": "p.Gln1711Lys",
"transcript": "XM_011519140.2",
"protein_id": "XP_011517442.1",
"transcript_support_level": null,
"aa_start": 1711,
"aa_end": null,
"aa_length": 1842,
"cds_start": 5131,
"cds_end": null,
"cds_length": 5529,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011519140.2"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 60,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.5125C>A",
"hgvs_p": "p.Gln1709Lys",
"transcript": "XM_047423992.1",
"protein_id": "XP_047279948.1",
"transcript_support_level": null,
"aa_start": 1709,
"aa_end": null,
"aa_length": 1840,
"cds_start": 5125,
"cds_end": null,
"cds_length": 5523,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423992.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.2866C>A",
"hgvs_p": "p.Gln956Lys",
"transcript": "XM_006717310.4",
"protein_id": "XP_006717373.1",
"transcript_support_level": null,
"aa_start": 956,
"aa_end": null,
"aa_length": 1087,
"cds_start": 2866,
"cds_end": null,
"cds_length": 3264,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717310.4"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "c.2752C>A",
"hgvs_p": "p.Gln918Lys",
"transcript": "XM_011519145.4",
"protein_id": "XP_011517447.1",
"transcript_support_level": null,
"aa_start": 918,
"aa_end": null,
"aa_length": 1049,
"cds_start": 2752,
"cds_end": null,
"cds_length": 3150,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011519145.4"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "n.715C>A",
"hgvs_p": null,
"transcript": "ENST00000468565.1",
"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": "ENST00000468565.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"hgvs_c": "n.554C>A",
"hgvs_p": null,
"transcript": "ENST00000490831.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000490831.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC105376224",
"gene_hgnc_id": null,
"hgvs_c": "n.350-1379G>T",
"hgvs_p": null,
"transcript": "XR_930255.3",
"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_930255.3"
}
],
"gene_symbol": "COL27A1",
"gene_hgnc_id": 22986,
"dbsnp": "rs1554829390",
"frequency_reference_population": 6.840975e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84097e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6334766149520874,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.563,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1753,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.905,
"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_032888.4",
"gene_symbol": "COL27A1",
"hgnc_id": 22986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5185C>A",
"hgvs_p": "p.Gln1729Lys"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XR_930255.3",
"gene_symbol": "LOC105376224",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.350-1379G>T",
"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
}