← Back to variant description
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: 2-165770196-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165770196&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165770196,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000392701.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "NM_004482.4",
"protein_id": "NP_004473.2",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 633,
"cds_start": 505,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 3436,
"mane_select": "ENST00000392701.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "ENST00000392701.8",
"protein_id": "ENSP00000376465.3",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 633,
"cds_start": 505,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 3436,
"mane_select": "NM_004482.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "ENST00000715282.1",
"protein_id": "ENSP00000520447.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 633,
"cds_start": 505,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 862,
"cdna_end": null,
"cdna_length": 2733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "ENST00000412248.5",
"protein_id": "ENSP00000412643.1",
"transcript_support_level": 5,
"aa_start": 169,
"aa_end": null,
"aa_length": 463,
"cds_start": 505,
"cds_end": null,
"cds_length": 1392,
"cdna_start": 1067,
"cdna_end": null,
"cdna_length": 1954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "XM_005246449.2",
"protein_id": "XP_005246506.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 633,
"cds_start": 505,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 1041,
"cdna_end": null,
"cdna_length": 3631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "XM_011510929.2",
"protein_id": "XP_011509231.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 633,
"cds_start": 505,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 817,
"cdna_end": null,
"cdna_length": 3407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "XM_017003770.2",
"protein_id": "XP_016859259.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 633,
"cds_start": 505,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 981,
"cdna_end": null,
"cdna_length": 3571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*",
"transcript": "XM_047443883.1",
"protein_id": "XP_047299839.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 401,
"cds_start": 505,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 1668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.*235C>T",
"hgvs_p": null,
"transcript": "ENST00000431484.1",
"protein_id": "ENSP00000397112.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 89,
"cds_start": -4,
"cds_end": null,
"cds_length": 270,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"dbsnp": "rs775341386",
"frequency_reference_population": 0.0000068154836,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000615658,
"gnomad_genomes_af": 0.0000131473,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6299999952316284,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.17000000178813934,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.63,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.793,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.17,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000392701.8",
"gene_symbol": "GALNT3",
"hgnc_id": 4125,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.505C>T",
"hgvs_p": "p.Arg169*"
}
],
"clinvar_disease": " 1, familial, hyperphosphatemic,Tumoral calcinosis,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Tumoral calcinosis, hyperphosphatemic, familial, 1|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}