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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: 14-52011047-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=52011047&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 52011047,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_007361.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.3551G>A",
"hgvs_p": "p.Gly1184Asp",
"transcript": "NM_007361.4",
"protein_id": "NP_031387.3",
"transcript_support_level": null,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3551,
"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": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.3551G>A",
"hgvs_p": "p.Gly1184Asp",
"transcript": "ENST00000216286.10",
"protein_id": "ENSP00000216286.4",
"transcript_support_level": 1,
"aa_start": 1184,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3551,
"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": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.1355G>A",
"hgvs_p": "p.Gly452Asp",
"transcript": "ENST00000556572.1",
"protein_id": "ENSP00000452190.1",
"transcript_support_level": 2,
"aa_start": 452,
"aa_end": null,
"aa_length": 643,
"cds_start": 1355,
"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": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.3632G>A",
"hgvs_p": "p.Gly1211Asp",
"transcript": "XM_005267405.5",
"protein_id": "XP_005267462.1",
"transcript_support_level": null,
"aa_start": 1211,
"aa_end": null,
"aa_length": 1402,
"cds_start": 3632,
"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": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.3488G>A",
"hgvs_p": "p.Gly1163Asp",
"transcript": "XM_005267406.5",
"protein_id": "XP_005267463.1",
"transcript_support_level": null,
"aa_start": 1163,
"aa_end": null,
"aa_length": 1354,
"cds_start": 3488,
"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": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_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.3407G>A",
"hgvs_p": "p.Gly1136Asp",
"transcript": "XM_005267407.5",
"protein_id": "XP_005267464.1",
"transcript_support_level": null,
"aa_start": 1136,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3407,
"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": [
"splice_region_variant",
"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.469G>A",
"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"
}
],
"gene_symbol": "NID2",
"gene_hgnc_id": 13389,
"dbsnp": "rs201074665",
"frequency_reference_population": 0.000037215672,
"hom_count_reference_population": 0,
"allele_count_reference_population": 60,
"gnomad_exomes_af": 0.0000349294,
"gnomad_genomes_af": 0.0000591576,
"gnomad_exomes_ac": 51,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.18138781189918518,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.33799999952316284,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.095,
"revel_prediction": "Benign",
"alphamissense_score": 0.1597,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.95,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.015751259904722,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_007361.4",
"gene_symbol": "NID2",
"hgnc_id": 13389,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3551G>A",
"hgvs_p": "p.Gly1184Asp"
}
],
"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
}