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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: 1-13731083-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=13731083&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 13731083,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_012231.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "NM_001393986.1",
"protein_id": "NP_001380915.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 1718,
"cds_start": 93,
"cds_end": null,
"cds_length": 5157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000311066.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393986.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "ENST00000311066.10",
"protein_id": "ENSP00000312352.6",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 1718,
"cds_start": 93,
"cds_end": null,
"cds_length": 5157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001393986.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000311066.10"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "ENST00000235372.11",
"protein_id": "ENSP00000235372.6",
"transcript_support_level": 1,
"aa_start": 31,
"aa_end": null,
"aa_length": 1718,
"cds_start": 93,
"cds_end": null,
"cds_length": 5157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000235372.11"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "NM_012231.5",
"protein_id": "NP_036363.2",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 1718,
"cds_start": 93,
"cds_end": null,
"cds_length": 5157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012231.5"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "NM_015866.6",
"protein_id": "NP_056950.2",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 1682,
"cds_start": 93,
"cds_end": null,
"cds_length": 5049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015866.6"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "NM_001135610.2",
"protein_id": "NP_001129082.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 226,
"cds_start": 93,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001135610.2"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "ENST00000376048.9",
"protein_id": "ENSP00000365216.5",
"transcript_support_level": 2,
"aa_start": 31,
"aa_end": null,
"aa_length": 226,
"cds_start": 93,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376048.9"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser",
"transcript": "ENST00000484063.6",
"protein_id": "ENSP00000423010.1",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 152,
"cds_start": 93,
"cds_end": null,
"cds_length": 460,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000484063.6"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.90G>T",
"hgvs_p": "p.Arg30Ser",
"transcript": "XM_047429996.1",
"protein_id": "XP_047285952.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 1717,
"cds_start": 90,
"cds_end": null,
"cds_length": 5154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429996.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.-130G>T",
"hgvs_p": null,
"transcript": "XM_047429994.1",
"protein_id": "XP_047285950.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1644,
"cds_start": null,
"cds_end": null,
"cds_length": 4935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429994.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "c.-130G>T",
"hgvs_p": null,
"transcript": "XM_047429995.1",
"protein_id": "XP_047285951.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1608,
"cds_start": null,
"cds_end": null,
"cds_length": 4827,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429995.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"hgvs_c": "n.66G>T",
"hgvs_p": null,
"transcript": "ENST00000491134.5",
"protein_id": "ENSP00000424253.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000491134.5"
}
],
"gene_symbol": "PRDM2",
"gene_hgnc_id": 9347,
"dbsnp": "rs184864123",
"frequency_reference_population": 0.0000020533826,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205338,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27277207374572754,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.36000001430511475,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.273,
"revel_prediction": "Benign",
"alphamissense_score": 0.3113,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.458,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.36,
"spliceai_max_prediction": "Uncertain_significance",
"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_012231.5",
"gene_symbol": "PRDM2",
"hgnc_id": 9347,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Arg31Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}