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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: 12-105235994-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=105235994&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 105235994,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_018171.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "NM_018171.5",
"protein_id": "NP_060641.2",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 664,
"cds_start": 19,
"cds_end": null,
"cds_length": 1995,
"cdna_start": 181,
"cdna_end": null,
"cdna_length": 3171,
"mane_select": "ENST00000258530.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "ENST00000258530.8",
"protein_id": "ENSP00000258530.3",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 664,
"cds_start": 19,
"cds_end": null,
"cds_length": 1995,
"cdna_start": 181,
"cdna_end": null,
"cdna_length": 3171,
"mane_select": "NM_018171.5",
"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": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "n.19C>T",
"hgvs_p": null,
"transcript": "ENST00000547439.5",
"protein_id": "ENSP00000449410.1",
"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": 3196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "NM_001251904.2",
"protein_id": "NP_001238833.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 670,
"cds_start": 19,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 181,
"cdna_end": null,
"cdna_length": 3189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "ENST00000551662.5",
"protein_id": "ENSP00000446917.1",
"transcript_support_level": 2,
"aa_start": 7,
"aa_end": null,
"aa_length": 670,
"cds_start": 19,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 90,
"cdna_end": null,
"cdna_length": 2190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "ENST00000553097.5",
"protein_id": "ENSP00000449767.1",
"transcript_support_level": 4,
"aa_start": 7,
"aa_end": null,
"aa_length": 143,
"cds_start": 19,
"cds_end": null,
"cds_length": 433,
"cdna_start": 100,
"cdna_end": null,
"cdna_length": 514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "XM_006719472.2",
"protein_id": "XP_006719535.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 623,
"cds_start": 19,
"cds_end": null,
"cds_length": 1872,
"cdna_start": 181,
"cdna_end": null,
"cdna_length": 3048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "XM_017019554.2",
"protein_id": "XP_016875043.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 617,
"cds_start": 19,
"cds_end": null,
"cds_length": 1854,
"cdna_start": 181,
"cdna_end": null,
"cdna_length": 3030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe",
"transcript": "XM_047429066.1",
"protein_id": "XP_047285022.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 397,
"cds_start": 19,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 181,
"cdna_end": null,
"cdna_length": 1418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"hgvs_c": "c.-6352C>T",
"hgvs_p": null,
"transcript": "XM_017019551.3",
"protein_id": "XP_016875040.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 651,
"cds_start": -4,
"cds_end": null,
"cds_length": 1956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9502,
"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": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "C12orf75",
"gene_hgnc_id": 35164,
"hgvs_c": "n.67+638G>A",
"hgvs_p": null,
"transcript": "ENST00000548458.6",
"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": 887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APPL2",
"gene_hgnc_id": 18242,
"dbsnp": null,
"frequency_reference_population": 0.000001816702,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000018167,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4894474148750305,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.233,
"revel_prediction": "Benign",
"alphamissense_score": 0.8386,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.08,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": 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_018171.5",
"gene_symbol": "APPL2",
"hgnc_id": 18242,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Leu7Phe"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000548458.6",
"gene_symbol": "C12orf75",
"hgnc_id": 35164,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.67+638G>A",
"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
}