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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: 20-62840573-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=62840573&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 62840573,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_001853.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.1896C>T",
"hgvs_p": "p.Asp632Asp",
"transcript": "NM_001853.4",
"protein_id": "NP_001844.3",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 684,
"cds_start": 1896,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000649368.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001853.4"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.1896C>T",
"hgvs_p": "p.Asp632Asp",
"transcript": "ENST00000649368.1",
"protein_id": "ENSP00000496793.1",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 684,
"cds_start": 1896,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001853.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000649368.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "n.407C>T",
"hgvs_p": null,
"transcript": "ENST00000467819.5",
"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": "pseudogene",
"feature": "ENST00000467819.5"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.1947C>T",
"hgvs_p": "p.Asp649Asp",
"transcript": "ENST00000934236.1",
"protein_id": "ENSP00000604295.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 701,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2106,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934236.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.1824C>T",
"hgvs_p": "p.Asp608Asp",
"transcript": "ENST00000894732.1",
"protein_id": "ENSP00000564791.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 660,
"cds_start": 1824,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894732.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.1749C>T",
"hgvs_p": "p.Asp583Asp",
"transcript": "ENST00000934235.1",
"protein_id": "ENSP00000604294.1",
"transcript_support_level": null,
"aa_start": 583,
"aa_end": null,
"aa_length": 635,
"cds_start": 1749,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934235.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.2073C>T",
"hgvs_p": "p.Asp691Asp",
"transcript": "XM_047439893.1",
"protein_id": "XP_047295849.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 743,
"cds_start": 2073,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439893.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.1335C>T",
"hgvs_p": "p.Asp445Asp",
"transcript": "XM_047439894.1",
"protein_id": "XP_047295850.1",
"transcript_support_level": null,
"aa_start": 445,
"aa_end": null,
"aa_length": 497,
"cds_start": 1335,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439894.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "n.651C>T",
"hgvs_p": null,
"transcript": "ENST00000462700.5",
"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": "ENST00000462700.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "n.1623C>T",
"hgvs_p": null,
"transcript": "ENST00000466192.5",
"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": "retained_intron",
"feature": "ENST00000466192.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "n.454C>T",
"hgvs_p": null,
"transcript": "ENST00000466532.1",
"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": "ENST00000466532.1"
}
],
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"dbsnp": "rs74830351",
"frequency_reference_population": 0.012551299,
"hom_count_reference_population": 171,
"allele_count_reference_population": 20240,
"gnomad_exomes_af": 0.0130533,
"gnomad_genomes_af": 0.00773917,
"gnomad_exomes_ac": 19061,
"gnomad_genomes_ac": 1179,
"gnomad_exomes_homalt": 162,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5600000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.911,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001853.4",
"gene_symbol": "COL9A3",
"hgnc_id": 2219,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1896C>T",
"hgvs_p": "p.Asp632Asp"
}
],
"clinvar_disease": "Connective tissue disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not specified|not provided|Connective tissue disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}