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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: 5-161326369-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=161326369&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 161326369,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000393959.6",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1190C>T",
"hgvs_p": "p.Thr397Met",
"transcript": "NM_001371727.1",
"protein_id": "NP_001358656.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 512,
"cds_start": 1190,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 7266,
"mane_select": "ENST00000393959.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1190C>T",
"hgvs_p": "p.Thr397Met",
"transcript": "ENST00000393959.6",
"protein_id": "ENSP00000377531.1",
"transcript_support_level": 1,
"aa_start": 397,
"aa_end": null,
"aa_length": 512,
"cds_start": 1190,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 7266,
"mane_select": "NM_001371727.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1077+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000353437.10",
"protein_id": "ENSP00000274546.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": -4,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1963,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1077+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000520240.5",
"protein_id": "ENSP00000429320.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": -4,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1190C>T",
"hgvs_p": "p.Thr397Met",
"transcript": "NM_021911.3",
"protein_id": "NP_068711.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 512,
"cds_start": 1190,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1688,
"cdna_end": null,
"cdna_length": 7682,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1190C>T",
"hgvs_p": "p.Thr397Met",
"transcript": "ENST00000274547.7",
"protein_id": "ENSP00000274547.2",
"transcript_support_level": 5,
"aa_start": 397,
"aa_end": null,
"aa_length": 512,
"cds_start": 1190,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 1366,
"cdna_end": null,
"cdna_length": 7367,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "n.1272C>T",
"hgvs_p": null,
"transcript": "ENST00000674514.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1077+4514C>T",
"hgvs_p": null,
"transcript": "NM_000813.3",
"protein_id": "NP_000804.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": -4,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1077+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000675303.1",
"protein_id": "ENSP00000502748.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": -4,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.1077+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000675773.1",
"protein_id": "ENSP00000502701.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 474,
"cds_start": -4,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.888+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000517901.5",
"protein_id": "ENSP00000430532.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 411,
"cds_start": -4,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.825+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000675381.1",
"protein_id": "ENSP00000501968.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 390,
"cds_start": -4,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.597+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000517547.5",
"protein_id": "ENSP00000429750.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 314,
"cds_start": -4,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "c.327+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000675746.1",
"protein_id": "ENSP00000502391.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 204,
"cds_start": -4,
"cds_end": null,
"cds_length": 617,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"hgvs_c": "n.*536+4514C>T",
"hgvs_p": null,
"transcript": "ENST00000675081.1",
"protein_id": "ENSP00000502207.1",
"transcript_support_level": null,
"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": 5620,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GABRB2",
"gene_hgnc_id": 4082,
"dbsnp": "rs375083192",
"frequency_reference_population": 0.000087400666,
"hom_count_reference_population": 0,
"allele_count_reference_population": 141,
"gnomad_exomes_af": 0.0000903509,
"gnomad_genomes_af": 0.0000590978,
"gnomad_exomes_ac": 132,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15780529379844666,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.0820000022649765,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.124,
"revel_prediction": "Benign",
"alphamissense_score": 0.1399,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.945,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0018934278623642,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000393959.6",
"gene_symbol": "GABRB2",
"hgnc_id": 4082,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1190C>T",
"hgvs_p": "p.Thr397Met"
}
],
"clinvar_disease": "Intellectual disability",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Intellectual disability",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}