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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: 7-94427629-C-CCCCCCTGGT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=94427629&ref=C&alt=CCCCCCTGGT&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM4",
"PP3"
],
"effects": [
"disruptive_inframe_insertion"
],
"gene_symbol": "COL1A2",
"hgnc_id": 2198,
"hgvs_c": "c.3279_3287dupTCCCCCTGG",
"hgvs_p": "p.Gly1096_Pro1097insProProGly",
"inheritance_mode": "AD,AR,Unknown",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_000089.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM4,PP3",
"acmg_score": 7,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "CCCCCCTGGT",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "7",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " 1, classic type,Ehlers-Danlos syndrome,Osteogenesis imperfecta type I",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 1366,
"aa_ref": "G",
"aa_start": 1096,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5072,
"cdna_start": 3425,
"cds_end": null,
"cds_length": 4101,
"cds_start": 3288,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 52,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "NM_000089.4",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3279_3287dupTCCCCCTGG",
"hgvs_p": "p.Gly1096_Pro1097insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000297268.11",
"protein_coding": true,
"protein_id": "NP_000080.2",
"strand": true,
"transcript": "NM_000089.4",
"transcript_support_level": null
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 1366,
"aa_ref": "G",
"aa_start": 1096,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5072,
"cdna_start": 3425,
"cds_end": null,
"cds_length": 4101,
"cds_start": 3288,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 52,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000297268.11",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3279_3287dupTCCCCCTGG",
"hgvs_p": "p.Gly1096_Pro1097insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000089.4",
"protein_coding": true,
"protein_id": "ENSP00000297268.6",
"strand": true,
"transcript": "ENST00000297268.11",
"transcript_support_level": 1
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "G",
"aa_start": 1095,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5144,
"cdna_start": 3497,
"cds_end": null,
"cds_length": 4098,
"cds_start": 3285,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 52,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000959377.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3276_3284dupTCCCCCTGG",
"hgvs_p": "p.Gly1095_Pro1096insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629436.1",
"strand": true,
"transcript": "ENST00000959377.1",
"transcript_support_level": null
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "G",
"aa_start": 1096,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4550,
"cdna_start": 3425,
"cds_end": null,
"cds_length": 4098,
"cds_start": 3288,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 52,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000959379.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3279_3287dupTCCCCCTGG",
"hgvs_p": "p.Gly1096_Pro1097insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629438.1",
"strand": true,
"transcript": "ENST00000959379.1",
"transcript_support_level": null
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 1361,
"aa_ref": "G",
"aa_start": 1091,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5005,
"cdna_start": 3366,
"cds_end": null,
"cds_length": 4086,
"cds_start": 3273,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 52,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000959378.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3264_3272dupTCCCCCTGG",
"hgvs_p": "p.Gly1091_Pro1092insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629437.1",
"strand": true,
"transcript": "ENST00000959378.1",
"transcript_support_level": null
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 1348,
"aa_ref": "G",
"aa_start": 1078,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4447,
"cdna_start": 3371,
"cds_end": null,
"cds_length": 4047,
"cds_start": 3234,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000959382.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3225_3233dupTCCCCCTGG",
"hgvs_p": "p.Gly1078_Pro1079insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629441.1",
"strand": true,
"transcript": "ENST00000959382.1",
"transcript_support_level": null
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 1156,
"aa_ref": "G",
"aa_start": 886,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3871,
"cdna_start": 2795,
"cds_end": null,
"cds_length": 3471,
"cds_start": 2658,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 43,
"exon_rank": 40,
"exon_rank_end": null,
"feature": "ENST00000959381.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.2649_2657dupTCCCCCTGG",
"hgvs_p": "p.Gly886_Pro887insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629440.1",
"strand": true,
"transcript": "ENST00000959381.1",
"transcript_support_level": null
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 955,
"aa_ref": "G",
"aa_start": 685,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": 2147,
"cds_end": null,
"cds_length": 2868,
"cds_start": 2055,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 36,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "ENST00000959383.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.2046_2054dupTCCCCCTGG",
"hgvs_p": "p.Gly685_Pro686insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629442.1",
"strand": true,
"transcript": "ENST00000959383.1",
"transcript_support_level": null
},
{
"aa_alt": "GPPG",
"aa_end": null,
"aa_length": 685,
"aa_ref": "G",
"aa_start": 415,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2465,
"cdna_start": 1338,
"cds_end": null,
"cds_length": 2058,
"cds_start": 1245,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_count": 25,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000959380.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.1236_1244dupTCCCCCTGG",
"hgvs_p": "p.Gly415_Pro416insProProGly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629439.1",
"strand": true,
"transcript": "ENST00000959380.1",
"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": 1123,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000464916.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.327_335dupTCCCCCTGG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000464916.1",
"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": 5993,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000481570.5",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.4060_4068dupTCCCCCTGG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000481570.5",
"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": 380,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000488121.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.*137_*138insCCCCCTGGT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000488121.1",
"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": 599,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000492110.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.*122_*123insCCCCCTGGT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000492110.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs74315103",
"effect": "disruptive_inframe_insertion",
"frequency_reference_population": 0.0000013683579,
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136836,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": "Ehlers-Danlos syndrome, classic type, 1;Osteogenesis imperfecta type I",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"pos": 94427629,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_000089.4"
}
]
}