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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: 9-128633931-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128633931&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DYNC2I2",
"hgnc_id": 28296,
"hgvs_c": "c.1424T>C",
"hgvs_p": "p.Leu475Ser",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_052844.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 9,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0624,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"chr": "9",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Short-rib thoracic dysplasia 11 with or without polydactyly",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.032591283321380615,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 536,
"aa_ref": "L",
"aa_start": 475,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1823,
"cdna_start": 1545,
"cds_end": null,
"cds_length": 1611,
"cds_start": 1424,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_052844.4",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1424T>C",
"hgvs_p": "p.Leu475Ser",
"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": "S",
"aa_end": null,
"aa_length": 536,
"aa_ref": "L",
"aa_start": 475,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1823,
"cdna_start": 1545,
"cds_end": null,
"cds_length": 1611,
"cds_start": 1424,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000372715.7",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1424T>C",
"hgvs_p": "p.Leu475Ser",
"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": "S",
"aa_end": null,
"aa_length": 535,
"aa_ref": "L",
"aa_start": 474,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1703,
"cdna_start": 1427,
"cds_end": null,
"cds_length": 1608,
"cds_start": 1421,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000946364.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1421T>C",
"hgvs_p": "p.Leu474Ser",
"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": "S",
"aa_end": null,
"aa_length": 530,
"aa_ref": "L",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1681,
"cdna_start": 1406,
"cds_end": null,
"cds_length": 1593,
"cds_start": 1406,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000925011.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1406T>C",
"hgvs_p": "p.Leu469Ser",
"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": "S",
"aa_end": null,
"aa_length": 527,
"aa_ref": "L",
"aa_start": 466,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1707,
"cdna_start": 1425,
"cds_end": null,
"cds_length": 1584,
"cds_start": 1397,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000854292.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1397T>C",
"hgvs_p": "p.Leu466Ser",
"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": "S",
"aa_end": null,
"aa_length": 508,
"aa_ref": "L",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1625,
"cdna_start": 1340,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1340,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000925010.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1340T>C",
"hgvs_p": "p.Leu447Ser",
"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": "S",
"aa_end": null,
"aa_length": 499,
"aa_ref": "L",
"aa_start": 438,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1583,
"cdna_start": 1313,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1313,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000946365.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1313T>C",
"hgvs_p": "p.Leu438Ser",
"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": "S",
"aa_end": null,
"aa_length": 447,
"aa_ref": "L",
"aa_start": 386,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1428,
"cdna_start": 1157,
"cds_end": null,
"cds_length": 1344,
"cds_start": 1157,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000854293.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1157T>C",
"hgvs_p": "p.Leu386Ser",
"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": "S",
"aa_end": null,
"aa_length": 536,
"aa_ref": "L",
"aa_start": 475,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1929,
"cdna_start": 1651,
"cds_end": null,
"cds_length": 1611,
"cds_start": 1424,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047424057.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1424T>C",
"hgvs_p": "p.Leu475Ser",
"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": "S",
"aa_end": null,
"aa_length": 508,
"aa_ref": "L",
"aa_start": 447,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1845,
"cdna_start": 1567,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1340,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011519179.3",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.1340T>C",
"hgvs_p": "p.Leu447Ser",
"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": "rs748451019",
"effect": "missense_variant",
"frequency_reference_population": 0.0000055793057,
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.0000047917,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131366,
"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": "Uncertain significance",
"phenotype_combined": "Short-rib thoracic dysplasia 11 with or without polydactyly",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.261,
"pos": 128633931,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.054,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_052844.4"
}
]
}