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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: 3-119609526-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=119609526&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 119609526,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_015900.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.512T>G",
"hgvs_p": "p.Val171Gly",
"transcript": "NM_015900.4",
"protein_id": "NP_056984.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 456,
"cds_start": 512,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000273371.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015900.4"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.512T>G",
"hgvs_p": "p.Val171Gly",
"transcript": "ENST00000273371.9",
"protein_id": "ENSP00000273371.4",
"transcript_support_level": 1,
"aa_start": 171,
"aa_end": null,
"aa_length": 456,
"cds_start": 512,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015900.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000273371.9"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "ENST00000494440.5",
"protein_id": "ENSP00000418793.1",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 440,
"cds_start": 464,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494440.5"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "ENST00000495992.5",
"protein_id": "ENSP00000417326.1",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 440,
"cds_start": 464,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000495992.5"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.512T>G",
"hgvs_p": "p.Val171Gly",
"transcript": "ENST00000874105.1",
"protein_id": "ENSP00000544164.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 497,
"cds_start": 512,
"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": "ENST00000874105.1"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.512T>G",
"hgvs_p": "p.Val171Gly",
"transcript": "ENST00000874106.1",
"protein_id": "ENSP00000544165.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 470,
"cds_start": 512,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874106.1"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "NM_001206960.2",
"protein_id": "NP_001193889.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 440,
"cds_start": 464,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206960.2"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.464T>G",
"hgvs_p": "p.Val155Gly",
"transcript": "NM_001293225.2",
"protein_id": "NP_001280154.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 440,
"cds_start": 464,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001293225.2"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.512T>G",
"hgvs_p": "p.Val171Gly",
"transcript": "ENST00000874104.1",
"protein_id": "ENSP00000544163.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 422,
"cds_start": 512,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874104.1"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.512T>G",
"hgvs_p": "p.Val171Gly",
"transcript": "ENST00000874108.1",
"protein_id": "ENSP00000544167.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 400,
"cds_start": 512,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874108.1"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.110T>G",
"hgvs_p": "p.Val37Gly",
"transcript": "ENST00000475963.1",
"protein_id": "ENSP00000417295.1",
"transcript_support_level": 5,
"aa_start": 37,
"aa_end": null,
"aa_length": 224,
"cds_start": 110,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000475963.1"
},
{
"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": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.-8T>G",
"hgvs_p": null,
"transcript": "NM_001206961.2",
"protein_id": "NP_001193890.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 283,
"cds_start": null,
"cds_end": null,
"cds_length": 852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206961.2"
},
{
"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": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.-8T>G",
"hgvs_p": null,
"transcript": "ENST00000488919.5",
"protein_id": "ENSP00000420625.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 283,
"cds_start": null,
"cds_end": null,
"cds_length": 852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000488919.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.-8T>G",
"hgvs_p": null,
"transcript": "XM_017006572.2",
"protein_id": "XP_016862061.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 283,
"cds_start": null,
"cds_end": null,
"cds_length": 852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006572.2"
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "c.74-3491T>G",
"hgvs_p": null,
"transcript": "ENST00000874107.1",
"protein_id": "ENSP00000544166.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 293,
"cds_start": null,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874107.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"hgvs_c": "n.541T>G",
"hgvs_p": null,
"transcript": "NR_120610.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_120610.2"
}
],
"gene_symbol": "PLA1A",
"gene_hgnc_id": 17661,
"dbsnp": "rs763712636",
"frequency_reference_population": 0.0000027378396,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273784,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9623982310295105,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.918,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6381,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.159,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_015900.4",
"gene_symbol": "PLA1A",
"hgnc_id": 17661,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.512T>G",
"hgvs_p": "p.Val171Gly"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}