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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: 9-98826816-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=98826816&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 98826816,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000375011.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.606C>T",
"hgvs_p": "p.Ala202Ala",
"transcript": "NM_024642.5",
"protein_id": "NP_078918.3",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 581,
"cds_start": 606,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 635,
"cdna_end": null,
"cdna_length": 2764,
"mane_select": "ENST00000375011.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.606C>T",
"hgvs_p": "p.Ala202Ala",
"transcript": "ENST00000375011.4",
"protein_id": "ENSP00000364150.3",
"transcript_support_level": 1,
"aa_start": 202,
"aa_end": null,
"aa_length": 581,
"cds_start": 606,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 635,
"cdna_end": null,
"cdna_length": 2764,
"mane_select": "NM_024642.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.384C>T",
"hgvs_p": "p.Ala128Ala",
"transcript": "XM_011519018.3",
"protein_id": "XP_011517320.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 507,
"cds_start": 384,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1279,
"cdna_end": null,
"cdna_length": 3408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.354C>T",
"hgvs_p": "p.Ala118Ala",
"transcript": "XM_017015133.1",
"protein_id": "XP_016870622.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 497,
"cds_start": 354,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 2495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "n.*37C>T",
"hgvs_p": null,
"transcript": "ENST00000610463.1",
"protein_id": "ENSP00000477657.1",
"transcript_support_level": 4,
"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": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.-286C>T",
"hgvs_p": null,
"transcript": "XM_006717287.1",
"protein_id": "XP_006717350.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 284,
"cds_start": -4,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.-286C>T",
"hgvs_p": null,
"transcript": "XM_047423871.1",
"protein_id": "XP_047279827.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 284,
"cds_start": -4,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "n.*37C>T",
"hgvs_p": null,
"transcript": "ENST00000610463.1",
"protein_id": "ENSP00000477657.1",
"transcript_support_level": 4,
"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": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.-135C>T",
"hgvs_p": null,
"transcript": "XM_011519020.2",
"protein_id": "XP_011517322.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 345,
"cds_start": -4,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"dbsnp": "rs1060504771",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6700000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.972,
"phylop100way_prediction": "Benign",
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 13,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000375011.4",
"gene_symbol": "GALNT12",
"hgnc_id": 19877,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.606C>T",
"hgvs_p": "p.Ala202Ala"
}
],
"clinvar_disease": "GALNT12-related disorder,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not provided|not specified|GALNT12-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}