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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: 9-128634259-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128634259&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DYNC2I2",
"hgnc_id": 28296,
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Trp",
"inheritance_mode": "AR",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_052844.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 35,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.5307,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.1,
"chr": "9",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Short-rib thoracic dysplasia 11 with or without polydactyly,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9075022339820862,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 536,
"aa_ref": "R",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1823,
"cdna_start": 1460,
"cds_end": null,
"cds_length": 1611,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_052844.4",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000372715.7",
"protein_coding": true,
"protein_id": "NP_443076.2",
"strand": false,
"transcript": "NM_052844.4",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 536,
"aa_ref": "R",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1823,
"cdna_start": 1460,
"cds_end": null,
"cds_length": 1611,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000372715.7",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_052844.4",
"protein_coding": true,
"protein_id": "ENSP00000361800.2",
"strand": false,
"transcript": "ENST00000372715.7",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 535,
"aa_ref": "R",
"aa_start": 446,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1703,
"cdna_start": 1342,
"cds_end": null,
"cds_length": 1608,
"cds_start": 1336,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000946364.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1336C>T",
"hgvs_p": "p.Arg446Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616423.1",
"strand": false,
"transcript": "ENST00000946364.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 530,
"aa_ref": "R",
"aa_start": 441,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1681,
"cdna_start": 1321,
"cds_end": null,
"cds_length": 1593,
"cds_start": 1321,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000925011.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1321C>T",
"hgvs_p": "p.Arg441Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595070.1",
"strand": false,
"transcript": "ENST00000925011.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 527,
"aa_ref": "R",
"aa_start": 438,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1707,
"cdna_start": 1340,
"cds_end": null,
"cds_length": 1584,
"cds_start": 1312,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000854292.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1312C>T",
"hgvs_p": "p.Arg438Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524351.1",
"strand": false,
"transcript": "ENST00000854292.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 508,
"aa_ref": "R",
"aa_start": 419,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1625,
"cdna_start": 1255,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1255,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000925010.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1255C>T",
"hgvs_p": "p.Arg419Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595069.1",
"strand": false,
"transcript": "ENST00000925010.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 499,
"aa_ref": "R",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1583,
"cdna_start": 1228,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1228,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000946365.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1228C>T",
"hgvs_p": "p.Arg410Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616424.1",
"strand": false,
"transcript": "ENST00000946365.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 447,
"aa_ref": "R",
"aa_start": 358,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1428,
"cdna_start": 1072,
"cds_end": null,
"cds_length": 1344,
"cds_start": 1072,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000854293.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1072C>T",
"hgvs_p": "p.Arg358Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524352.1",
"strand": false,
"transcript": "ENST00000854293.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 536,
"aa_ref": "R",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1929,
"cdna_start": 1566,
"cds_end": null,
"cds_length": 1611,
"cds_start": 1339,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047424057.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1339C>T",
"hgvs_p": "p.Arg447Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047280013.1",
"strand": false,
"transcript": "XM_047424057.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 508,
"aa_ref": "R",
"aa_start": 419,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1845,
"cdna_start": 1482,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1255,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011519179.3",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1255C>T",
"hgvs_p": "p.Arg419Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011517481.1",
"strand": false,
"transcript": "XM_011519179.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587777093",
"effect": "missense_variant",
"frequency_reference_population": 0.000021689286,
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"gnomad_exomes_ac": 29,
"gnomad_exomes_af": 0.0000198424,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000394254,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Short-rib thoracic dysplasia 11 with or without polydactyly|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.886,
"pos": 128634259,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.651,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_052844.4"
}
]
}