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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: 9-128634895-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128634895&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 128634895,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_052844.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1008C>T",
"hgvs_p": "p.Gly336Gly",
"transcript": "NM_052844.4",
"protein_id": "NP_443076.2",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 536,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372715.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_052844.4"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1008C>T",
"hgvs_p": "p.Gly336Gly",
"transcript": "ENST00000372715.7",
"protein_id": "ENSP00000361800.2",
"transcript_support_level": 1,
"aa_start": 336,
"aa_end": null,
"aa_length": 536,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_052844.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372715.7"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1005C>T",
"hgvs_p": "p.Gly335Gly",
"transcript": "ENST00000946364.1",
"protein_id": "ENSP00000616423.1",
"transcript_support_level": null,
"aa_start": 335,
"aa_end": null,
"aa_length": 535,
"cds_start": 1005,
"cds_end": null,
"cds_length": 1608,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946364.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.990C>T",
"hgvs_p": "p.Gly330Gly",
"transcript": "ENST00000925011.1",
"protein_id": "ENSP00000595070.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 530,
"cds_start": 990,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925011.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.981C>T",
"hgvs_p": "p.Gly327Gly",
"transcript": "ENST00000854292.1",
"protein_id": "ENSP00000524351.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 527,
"cds_start": 981,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854292.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.924C>T",
"hgvs_p": "p.Gly308Gly",
"transcript": "ENST00000925010.1",
"protein_id": "ENSP00000595069.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 508,
"cds_start": 924,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925010.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.897C>T",
"hgvs_p": "p.Gly299Gly",
"transcript": "ENST00000946365.1",
"protein_id": "ENSP00000616424.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 499,
"cds_start": 897,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946365.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.741C>T",
"hgvs_p": "p.Gly247Gly",
"transcript": "ENST00000854293.1",
"protein_id": "ENSP00000524352.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 447,
"cds_start": 741,
"cds_end": null,
"cds_length": 1344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854293.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.1008C>T",
"hgvs_p": "p.Gly336Gly",
"transcript": "XM_047424057.1",
"protein_id": "XP_047280013.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 536,
"cds_start": 1008,
"cds_end": null,
"cds_length": 1611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424057.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "c.924C>T",
"hgvs_p": "p.Gly308Gly",
"transcript": "XM_011519179.3",
"protein_id": "XP_011517481.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 508,
"cds_start": 924,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011519179.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"hgvs_c": "n.601C>T",
"hgvs_p": null,
"transcript": "ENST00000483181.1",
"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": "ENST00000483181.1"
}
],
"gene_symbol": "DYNC2I2",
"gene_hgnc_id": 28296,
"dbsnp": "rs146077746",
"frequency_reference_population": 0.0012877953,
"hom_count_reference_population": 3,
"allele_count_reference_population": 2077,
"gnomad_exomes_af": 0.0013057,
"gnomad_genomes_af": 0.00111609,
"gnomad_exomes_ac": 1907,
"gnomad_genomes_ac": 170,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.28999999165534973,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.585,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.29,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_052844.4",
"gene_symbol": "DYNC2I2",
"hgnc_id": 28296,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1008C>T",
"hgvs_p": "p.Gly336Gly"
}
],
"clinvar_disease": "Short-rib thoracic dysplasia 11 with or without polydactyly,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"phenotype_combined": "Short-rib thoracic dysplasia 11 with or without polydactyly|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}