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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: 14-52010903-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=52010903&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 52010903,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_007361.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"hgvs_c": "c.3695G>C",
"hgvs_p": "p.Arg1232Pro",
"transcript": "NM_007361.4",
"protein_id": "NP_031387.3",
"transcript_support_level": null,
"aa_start": 1232,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3695,
"cds_end": null,
"cds_length": 4128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000216286.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007361.4"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"hgvs_c": "c.3695G>C",
"hgvs_p": "p.Arg1232Pro",
"transcript": "ENST00000216286.10",
"protein_id": "ENSP00000216286.4",
"transcript_support_level": 1,
"aa_start": 1232,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3695,
"cds_end": null,
"cds_length": 4128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007361.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000216286.10"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"hgvs_c": "c.1499G>C",
"hgvs_p": "p.Arg500Pro",
"transcript": "ENST00000556572.1",
"protein_id": "ENSP00000452190.1",
"transcript_support_level": 2,
"aa_start": 500,
"aa_end": null,
"aa_length": 643,
"cds_start": 1499,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000556572.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"hgvs_c": "c.3776G>C",
"hgvs_p": "p.Arg1259Pro",
"transcript": "XM_005267405.5",
"protein_id": "XP_005267462.1",
"transcript_support_level": null,
"aa_start": 1259,
"aa_end": null,
"aa_length": 1402,
"cds_start": 3776,
"cds_end": null,
"cds_length": 4209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005267405.5"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"hgvs_c": "c.3632G>C",
"hgvs_p": "p.Arg1211Pro",
"transcript": "XM_005267406.5",
"protein_id": "XP_005267463.1",
"transcript_support_level": null,
"aa_start": 1211,
"aa_end": null,
"aa_length": 1354,
"cds_start": 3632,
"cds_end": null,
"cds_length": 4065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005267406.5"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"hgvs_c": "c.3551G>C",
"hgvs_p": "p.Arg1184Pro",
"transcript": "XM_005267407.5",
"protein_id": "XP_005267464.1",
"transcript_support_level": null,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3551,
"cds_end": null,
"cds_length": 3984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005267407.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"hgvs_c": "n.613G>C",
"hgvs_p": null,
"transcript": "ENST00000553297.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000553297.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTRAF",
"gene_hgnc_id": 23169,
"hgvs_c": "c.*6387C>G",
"hgvs_p": null,
"transcript": "NM_016039.3",
"protein_id": "NP_057123.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 244,
"cds_start": null,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261700.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016039.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTRAF",
"gene_hgnc_id": 23169,
"hgvs_c": "c.*6387C>G",
"hgvs_p": null,
"transcript": "ENST00000261700.8",
"protein_id": "ENSP00000261700.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 244,
"cds_start": null,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016039.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261700.8"
}
],
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"dbsnp": "rs779100862",
"frequency_reference_population": 0.0000013687005,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013687,
"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": 0.9377926588058472,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.925,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9938,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.844,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.07,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_007361.4",
"gene_symbol": "NID2",
"hgnc_id": 13389,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3695G>C",
"hgvs_p": "p.Arg1232Pro"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016039.3",
"gene_symbol": "RTRAF",
"hgnc_id": 23169,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*6387C>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}