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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: 15-41841521-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=41841521&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "JMJD7-PLA2G4B",
"hgnc_id": 34449,
"hgvs_c": "c.1133G>T",
"hgvs_p": "p.Arg378Leu",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_005090.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PLA2G4B",
"hgnc_id": 9036,
"hgvs_c": "c.440G>T",
"hgvs_p": "p.Arg147Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001114633.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.4846,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.17,
"chr": "15",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6531918048858643,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 781,
"aa_ref": "R",
"aa_start": 147,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2696,
"cdna_start": 507,
"cds_end": null,
"cds_length": 2346,
"cds_start": 440,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001114633.2",
"gene_hgnc_id": 9036,
"gene_symbol": "PLA2G4B",
"hgvs_c": "c.440G>T",
"hgvs_p": "p.Arg147Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000458483.4",
"protein_coding": true,
"protein_id": "NP_001108105.1",
"strand": true,
"transcript": "NM_001114633.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 781,
"aa_ref": "R",
"aa_start": 147,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2696,
"cdna_start": 507,
"cds_end": null,
"cds_length": 2346,
"cds_start": 440,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000458483.4",
"gene_hgnc_id": 9036,
"gene_symbol": "PLA2G4B",
"hgvs_c": "c.440G>T",
"hgvs_p": "p.Arg147Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001114633.2",
"protein_coding": true,
"protein_id": "ENSP00000416610.1",
"strand": true,
"transcript": "ENST00000458483.4",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "R",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3331,
"cdna_start": 1142,
"cds_end": null,
"cds_length": 3039,
"cds_start": 1133,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000382448.8",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "c.1133G>T",
"hgvs_p": "p.Arg378Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000371886.4",
"strand": true,
"transcript": "ENST00000382448.8",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "R",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3355,
"cdna_start": 1166,
"cds_end": null,
"cds_length": 3039,
"cds_start": 1133,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_005090.4",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "c.1133G>T",
"hgvs_p": "p.Arg378Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_005081.1",
"strand": true,
"transcript": "NM_005090.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 893,
"aa_ref": "R",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3168,
"cdna_start": 1166,
"cds_end": null,
"cds_length": 2682,
"cds_start": 1133,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001198588.2",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "c.1133G>T",
"hgvs_p": "p.Arg378Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001185517.1",
"strand": true,
"transcript": "NM_001198588.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 893,
"aa_ref": "R",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2966,
"cdna_start": 1141,
"cds_end": null,
"cds_length": 2682,
"cds_start": 1133,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000342159.6",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "c.1133G>T",
"hgvs_p": "p.Arg378Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000342785.4",
"strand": true,
"transcript": "ENST00000342159.6",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 781,
"aa_ref": "R",
"aa_start": 147,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2985,
"cdna_start": 792,
"cds_end": null,
"cds_length": 2346,
"cds_start": 440,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000452633.5",
"gene_hgnc_id": 9036,
"gene_symbol": "PLA2G4B",
"hgvs_c": "c.440G>T",
"hgvs_p": "p.Arg147Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000396045.1",
"strand": true,
"transcript": "ENST00000452633.5",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 780,
"aa_ref": "R",
"aa_start": 147,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2698,
"cdna_start": 512,
"cds_end": null,
"cds_length": 2343,
"cds_start": 440,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000880478.1",
"gene_hgnc_id": 9036,
"gene_symbol": "PLA2G4B",
"hgvs_c": "c.440G>T",
"hgvs_p": "p.Arg147Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550537.1",
"strand": true,
"transcript": "ENST00000880478.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1530,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000461382.5",
"gene_hgnc_id": 9036,
"gene_symbol": "PLA2G4B",
"hgvs_c": "n.784G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000461382.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3178,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000487292.1",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "n.*782G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000424127.1",
"strand": true,
"transcript": "ENST00000487292.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 7218,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000490848.5",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "n.4642G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000490848.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 7227,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000491746.5",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "n.4468G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000491746.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3178,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000487292.1",
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"hgvs_c": "n.*782G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000424127.1",
"strand": true,
"transcript": "ENST00000487292.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs372615666",
"effect": "missense_variant",
"frequency_reference_population": 6.8406285e-7,
"gene_hgnc_id": 34449,
"gene_symbol": "JMJD7-PLA2G4B",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84063e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.78,
"pos": 41841521,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.18,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_005090.4"
}
]
}