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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: 8-53235088-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=53235088&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 53235088,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000912.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "c.281C>A",
"hgvs_p": "p.Thr94Asn",
"transcript": "NM_000912.5",
"protein_id": "NP_000903.2",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 380,
"cds_start": 281,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 4954,
"mane_select": "ENST00000265572.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "c.281C>A",
"hgvs_p": "p.Thr94Asn",
"transcript": "ENST00000265572.8",
"protein_id": "ENSP00000265572.3",
"transcript_support_level": 1,
"aa_start": 94,
"aa_end": null,
"aa_length": 380,
"cds_start": 281,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 4954,
"mane_select": "NM_000912.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "c.281C>A",
"hgvs_p": "p.Thr94Asn",
"transcript": "ENST00000520287.5",
"protein_id": "ENSP00000429706.1",
"transcript_support_level": 1,
"aa_start": 94,
"aa_end": null,
"aa_length": 380,
"cds_start": 281,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 656,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "c.14C>A",
"hgvs_p": "p.Thr5Asn",
"transcript": "ENST00000524278.5",
"protein_id": "ENSP00000430923.1",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 291,
"cds_start": 14,
"cds_end": null,
"cds_length": 876,
"cdna_start": 239,
"cdna_end": null,
"cdna_length": 1195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "n.*104C>A",
"hgvs_p": null,
"transcript": "ENST00000522508.1",
"protein_id": "ENSP00000428231.1",
"transcript_support_level": 1,
"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": 2041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "n.*104C>A",
"hgvs_p": null,
"transcript": "ENST00000522508.1",
"protein_id": "ENSP00000428231.1",
"transcript_support_level": 1,
"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": 2041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "c.281C>A",
"hgvs_p": "p.Thr94Asn",
"transcript": "NM_001318497.2",
"protein_id": "NP_001305426.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 409,
"cds_start": 281,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 4954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "c.281C>A",
"hgvs_p": "p.Thr94Asn",
"transcript": "ENST00000673285.2",
"protein_id": "ENSP00000500765.2",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 409,
"cds_start": 281,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 4954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"hgvs_c": "c.14C>A",
"hgvs_p": "p.Thr5Asn",
"transcript": "NM_001282904.2",
"protein_id": "NP_001269833.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 291,
"cds_start": 14,
"cds_end": null,
"cds_length": 876,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 5128,
"mane_select": null,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000254687",
"gene_hgnc_id": null,
"hgvs_c": "n.671-7440G>T",
"hgvs_p": null,
"transcript": "ENST00000524425.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OPRK1",
"gene_hgnc_id": 8154,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9660263061523438,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.536,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.899,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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_000912.5",
"gene_symbol": "OPRK1",
"hgnc_id": 8154,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.281C>A",
"hgvs_p": "p.Thr94Asn"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000524425.1",
"gene_symbol": "ENSG00000254687",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.671-7440G>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
}