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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: 4-7433319-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=7433319&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 7433319,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001085382.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSAPL1",
"gene_hgnc_id": 33131,
"hgvs_c": "c.1561G>A",
"hgvs_p": "p.Ala521Thr",
"transcript": "NM_001085382.2",
"protein_id": "NP_001078851.1",
"transcript_support_level": null,
"aa_start": 521,
"aa_end": null,
"aa_length": 521,
"cds_start": 1561,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1612,
"cdna_end": null,
"cdna_length": 4646,
"mane_select": "ENST00000319098.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSAPL1",
"gene_hgnc_id": 33131,
"hgvs_c": "c.1561G>A",
"hgvs_p": "p.Ala521Thr",
"transcript": "ENST00000319098.7",
"protein_id": "ENSP00000317445.4",
"transcript_support_level": 6,
"aa_start": 521,
"aa_end": null,
"aa_length": 521,
"cds_start": 1561,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 1612,
"cdna_end": null,
"cdna_length": 4646,
"mane_select": "NM_001085382.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "NM_020777.3",
"protein_id": "NP_065828.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1159,
"cds_start": -4,
"cds_end": null,
"cds_length": 3480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6152,
"mane_select": "ENST00000507866.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "ENST00000507866.6",
"protein_id": "ENSP00000422185.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1159,
"cds_start": -4,
"cds_end": null,
"cds_length": 3480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6152,
"mane_select": "NM_020777.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "n.163+36964C>T",
"hgvs_p": null,
"transcript": "ENST00000511199.1",
"protein_id": null,
"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": 532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "XM_005247987.5",
"protein_id": "XP_005248044.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1174,
"cds_start": -4,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6197,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "XM_011513514.3",
"protein_id": "XP_011511816.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1173,
"cds_start": -4,
"cds_end": null,
"cds_length": 3522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "XM_011513515.3",
"protein_id": "XP_011511817.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1173,
"cds_start": -4,
"cds_end": null,
"cds_length": 3522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "XM_047416006.1",
"protein_id": "XP_047271962.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1172,
"cds_start": -4,
"cds_end": null,
"cds_length": 3519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "XM_017008481.2",
"protein_id": "XP_016863970.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1166,
"cds_start": -4,
"cds_end": null,
"cds_length": 3501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "XM_047416007.1",
"protein_id": "XP_047271963.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1165,
"cds_start": -4,
"cds_end": null,
"cds_length": 3498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SORCS2",
"gene_hgnc_id": 16698,
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null,
"transcript": "XM_011513516.3",
"protein_id": "XP_011511818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1160,
"cds_start": -4,
"cds_end": null,
"cds_length": 3483,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6155,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PSAPL1",
"gene_hgnc_id": 33131,
"dbsnp": "rs1056786507",
"frequency_reference_population": 0.0000064003643,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000558239,
"gnomad_genomes_af": 0.0000131384,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07505440711975098,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.076,
"revel_prediction": "Benign",
"alphamissense_score": 0.0749,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.089,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001085382.2",
"gene_symbol": "PSAPL1",
"hgnc_id": 33131,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1561G>A",
"hgvs_p": "p.Ala521Thr"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_020777.3",
"gene_symbol": "SORCS2",
"hgnc_id": 16698,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.548+36964C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}