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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: 1-161983763-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=161983763&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "OLFML2B",
"hgnc_id": 24558,
"hgvs_c": "c.2171C>T",
"hgvs_p": "p.Thr724Ile",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_001347700.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": 0.8836,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.46,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8873436450958252,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 750,
"aa_ref": "T",
"aa_start": 722,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3175,
"cdna_start": 2604,
"cds_end": null,
"cds_length": 2253,
"cds_start": 2165,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_015441.3",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "c.2165C>T",
"hgvs_p": "p.Thr722Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000294794.8",
"protein_coding": true,
"protein_id": "NP_056256.1",
"strand": false,
"transcript": "NM_015441.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 750,
"aa_ref": "T",
"aa_start": 722,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3175,
"cdna_start": 2604,
"cds_end": null,
"cds_length": 2253,
"cds_start": 2165,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000294794.8",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "c.2165C>T",
"hgvs_p": "p.Thr722Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015441.3",
"protein_coding": true,
"protein_id": "ENSP00000294794.3",
"strand": false,
"transcript": "ENST00000294794.8",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 752,
"aa_ref": "T",
"aa_start": 724,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3181,
"cdna_start": 2610,
"cds_end": null,
"cds_length": 2259,
"cds_start": 2171,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001347700.2",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "c.2171C>T",
"hgvs_p": "p.Thr724Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001334629.1",
"strand": false,
"transcript": "NM_001347700.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 751,
"aa_ref": "T",
"aa_start": 723,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3178,
"cdna_start": 2607,
"cds_end": null,
"cds_length": 2256,
"cds_start": 2168,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001297713.2",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "c.2168C>T",
"hgvs_p": "p.Thr723Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001284642.1",
"strand": false,
"transcript": "NM_001297713.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 751,
"aa_ref": "T",
"aa_start": 723,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2685,
"cdna_start": 2378,
"cds_end": null,
"cds_length": 2256,
"cds_start": 2168,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000367940.2",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "c.2168C>T",
"hgvs_p": "p.Thr723Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000356917.2",
"strand": false,
"transcript": "ENST00000367940.2",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 233,
"aa_ref": "T",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1153,
"cdna_start": 943,
"cds_end": null,
"cds_length": 702,
"cds_start": 614,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000367938.1",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "c.614C>T",
"hgvs_p": "p.Thr205Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000356915.1",
"strand": false,
"transcript": "ENST00000367938.1",
"transcript_support_level": 2
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 510,
"aa_ref": "T",
"aa_start": 482,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4181,
"cdna_start": 3610,
"cds_end": null,
"cds_length": 1533,
"cds_start": 1445,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011509398.3",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "c.1445C>T",
"hgvs_p": "p.Thr482Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011507700.1",
"strand": false,
"transcript": "XM_011509398.3",
"transcript_support_level": null
},
{
"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": 559,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000525589.1",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "n.179C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000435212.1",
"strand": false,
"transcript": "ENST00000525589.1",
"transcript_support_level": 3
},
{
"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": 496,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000533556.1",
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"hgvs_c": "n.185C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000436707.1",
"strand": false,
"transcript": "ENST00000533556.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1482872581",
"effect": "missense_variant",
"frequency_reference_population": 0.0000020521325,
"gene_hgnc_id": 24558,
"gene_symbol": "OLFML2B",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000205213,
"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": "Pathogenic",
"phylop100way_score": 9.859,
"pos": 161983763,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.886,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001347700.2"
}
]
}