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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: 9-128636991-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128636991&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"effects": [
"stop_gained"
],
"gene_symbol": "DYNC2I2",
"hgnc_id": 28296,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_052844.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_score": 12,
"allele_count_reference_population": 22,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.55,
"chr": "9",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Short-rib thoracic dysplasia 11 with or without polydactyly",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.550000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 536,
"aa_ref": "Q",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1823,
"cdna_start": 593,
"cds_end": null,
"cds_length": 1611,
"cds_start": 472,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_052844.4",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"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": "*",
"aa_end": null,
"aa_length": 536,
"aa_ref": "Q",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1823,
"cdna_start": 593,
"cds_end": null,
"cds_length": 1611,
"cds_start": 472,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000372715.7",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"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": "*",
"aa_end": null,
"aa_length": 535,
"aa_ref": "Q",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1703,
"cdna_start": 478,
"cds_end": null,
"cds_length": 1608,
"cds_start": 472,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000946364.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"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": "*",
"aa_end": null,
"aa_length": 530,
"aa_ref": "Q",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1681,
"cdna_start": 472,
"cds_end": null,
"cds_length": 1593,
"cds_start": 472,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000925011.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"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": "*",
"aa_end": null,
"aa_length": 527,
"aa_ref": "Q",
"aa_start": 149,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1707,
"cdna_start": 473,
"cds_end": null,
"cds_length": 1584,
"cds_start": 445,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000854292.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.445C>T",
"hgvs_p": "p.Gln149*",
"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": "*",
"aa_end": null,
"aa_length": 508,
"aa_ref": "Q",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1625,
"cdna_start": 472,
"cds_end": null,
"cds_length": 1527,
"cds_start": 472,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000925010.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"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": "*",
"aa_end": null,
"aa_length": 499,
"aa_ref": "Q",
"aa_start": 149,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1583,
"cdna_start": 445,
"cds_end": null,
"cds_length": 1500,
"cds_start": 445,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000946365.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.445C>T",
"hgvs_p": "p.Gln149*",
"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": "*",
"aa_end": null,
"aa_length": 447,
"aa_ref": "Q",
"aa_start": 75,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1428,
"cdna_start": 223,
"cds_end": null,
"cds_length": 1344,
"cds_start": 223,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000854293.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.223C>T",
"hgvs_p": "p.Gln75*",
"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": "*",
"aa_end": null,
"aa_length": 536,
"aa_ref": "Q",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1929,
"cdna_start": 699,
"cds_end": null,
"cds_length": 1611,
"cds_start": 472,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047424057.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"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": "*",
"aa_end": null,
"aa_length": 508,
"aa_ref": "Q",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1845,
"cdna_start": 699,
"cds_end": null,
"cds_length": 1527,
"cds_start": 472,
"consequences": [
"stop_gained"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011519179.3",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Gln158*",
"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
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1039,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000451652.5",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "n.445C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000451652.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 714,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000473486.1",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "n.38C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000473486.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 739,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000419989.2",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "n.391-553C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000415421.1",
"strand": false,
"transcript": "ENST00000419989.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 745,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000480613.6",
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"hgvs_c": "n.391-553C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000480613.6",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587777097",
"effect": "stop_gained",
"frequency_reference_population": 0.00001363646,
"gene_hgnc_id": 28296,
"gene_symbol": "DYNC2I2",
"gnomad_exomes_ac": 18,
"gnomad_exomes_af": 0.0000123193,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262809,
"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",
"phenotype_combined": "Short-rib thoracic dysplasia 11 with or without polydactyly",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.945,
"pos": 128636991,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10000000149011612,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.1,
"transcript": "NM_052844.4"
}
]
}