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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: 9-128635116-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128635116&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 128635116,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_052844.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.957G>A",
"hgvs_p": "p.Leu319Leu",
"transcript": "NM_052844.4",
"protein_id": "NP_443076.2",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 536,
"cds_start": 957,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1078,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": "ENST00000372715.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.957G>A",
"hgvs_p": "p.Leu319Leu",
"transcript": "ENST00000372715.7",
"protein_id": "ENSP00000361800.2",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 536,
"cds_start": 957,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1078,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": "NM_052844.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.957G>A",
"hgvs_p": "p.Leu319Leu",
"transcript": "XM_047424057.1",
"protein_id": "XP_047280013.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 536,
"cds_start": 957,
"cds_end": null,
"cds_length": 1611,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 1929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.873G>A",
"hgvs_p": "p.Leu291Leu",
"transcript": "XM_011519179.3",
"protein_id": "XP_011517481.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 508,
"cds_start": 873,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 1100,
"cdna_end": null,
"cdna_length": 1845,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "n.550G>A",
"hgvs_p": null,
"transcript": "ENST00000483181.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "n.*382G>A",
"hgvs_p": null,
"transcript": "ENST00000419989.2",
"protein_id": "ENSP00000415421.1",
"transcript_support_level": 5,
"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": 739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "n.*207G>A",
"hgvs_p": null,
"transcript": "ENST00000473486.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"dbsnp": "rs75450756",
"frequency_reference_population": 0.004870017,
"hom_count_reference_population": 144,
"allele_count_reference_population": 7853,
"gnomad_exomes_af": 0.00477474,
"gnomad_genomes_af": 0.00578327,
"gnomad_exomes_ac": 6972,
"gnomad_genomes_ac": 881,
"gnomad_exomes_homalt": 120,
"gnomad_genomes_homalt": 24,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4000000059604645,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.854,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_052844.4",
"gene_symbol": "DYNC2I2",
"hgnc_id": 28296,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.957G>A",
"hgvs_p": "p.Leu319Leu"
}
],
"clinvar_disease": "Short-rib thoracic dysplasia 11 with or without polydactyly,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Short-rib thoracic dysplasia 11 with or without polydactyly|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}