Variant Annotation
Available parameters and response documentation is available here
GET /lookup/15-73027478-T-C?add-ACMG-annotation=1
{
"chromosome": "chr15",
"alt": "C",
"ref": "T",
"pos": 73027478,
"variant_id": "10190150730274780002",
"regions": {
"uniprot_regions": {
"version": "04-Oct-2024",
"items": [
{
"absolute_positon": 949181847,
"amino_acid": "M1-T8,R9-A26,A26-K52,A53-A74,A74-L111,L111-W135,E136-K153,A154-E196,E196-Q214,L215-K237,A238-A288,A289-V346,V346-K369,K369-E416,M417-G484,G484-K519",
"chromo": "chr15",
"colour": "255,0,0",
"description": null,
"length": 52267,
"position": 72978548,
"protein": "BBS4_HUMAN",
"type": "homo_sapiens proteome sequences",
"pub_med_references": null
},
{
"absolute_positon": 949227342,
"amino_acid": "G338-K519",
"chromo": "chr15",
"colour": "255,102,0",
"description": "Required for localization to centrosomes",
"length": 5883,
"position": 73024043,
"protein": "BBS4_HUMAN",
"type": "region of interest",
"pub_med_references": null
},
{
"absolute_positon": 949227345,
"amino_acid": "E339-N371",
"chromo": "chr15",
"colour": "153,0,255",
"description": "TPR 9",
"length": 4127,
"position": 73024046,
"protein": "BBS4_HUMAN",
"type": "repeat region",
"pub_med_references": null
}
]
}
},
"variant_type": "SNV",
"cytobands": "15q24.1",
"refseq_transcripts": [
{
"items": [
{
"name": "NM_033028.5",
"strand": "+",
"coding_impact": "missense",
"function": [
"coding"
],
"hgvs": "c.1061T>C",
"hgvs_p1": "I354T",
"hgvs_p3": "p.(Ile354Thr)",
"location": "exon 13 of 16 position 25 of 70",
"coding_location": "354 of 520",
"canonical": true,
"gene_symbol": "BBS4",
"splice_distance": "25",
"ensembl_support_level": null,
"ensembl_appris": null,
"mane_select": "ENST00000268057.9",
"mane_plus": null,
"uniprot_id": null
},
{
"name": "NR_045565.2",
"strand": "+",
"coding_impact": null,
"function": [
"non-coding exon"
],
"hgvs": null,
"hgvs_p1": null,
"hgvs_p3": null,
"location": "exon 14 of 17 position 25 of 70",
"coding_location": null,
"canonical": false,
"gene_symbol": "BBS4",
"splice_distance": "25",
"ensembl_support_level": null,
"ensembl_appris": null,
"mane_select": null,
"mane_plus": null,
"uniprot_id": null
},
{
"name": "NR_045566.2",
"strand": "+",
"coding_impact": null,
"function": [
"non-coding exon"
],
"hgvs": null,
"hgvs_p1": null,
"hgvs_p3": null,
"location": "exon 13 of 16 position 25 of 70",
"coding_location": null,
"canonical": false,
"gene_symbol": "BBS4",
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"ensembl_support_level": null,
"ensembl_appris": null,
"mane_select": null,
"mane_plus": null,
"uniprot_id": null
},
{
"name": "NM_001252678.2",
"strand": "+",
"coding_impact": "missense",
"function": [
"coding"
],
"hgvs": "c.545T>C",
"hgvs_p1": "I182T",
"hgvs_p3": "p.(Ile182Thr)",
"location": "exon 12 of 15 position 25 of 70",
"coding_location": "182 of 348",
"canonical": false,
"gene_symbol": "BBS4",
"splice_distance": "25",
"ensembl_support_level": null,
"ensembl_appris": null,
"mane_select": null,
"mane_plus": null,
"uniprot_id": null
},
{
"name": "NM_001320665.2",
"strand": "+",
"coding_impact": "missense",
"function": [
"coding"
],
"hgvs": "c.992T>C",
"hgvs_p1": "I331T",
"hgvs_p3": "p.(Ile331Thr)",
"location": "exon 12 of 15 position 25 of 70",
"coding_location": "331 of 497",
"canonical": false,
"gene_symbol": "BBS4",
"splice_distance": "25",
"ensembl_support_level": null,
"ensembl_appris": null,
"mane_select": null,
"mane_plus": null,
"uniprot_id": null
}
],
"version": "224"
}
],
"ensembl_transcripts": [
{
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{
"name": "ENST00000268057.4",
"strand": "+",
"coding_impact": "missense",
"function": [
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],
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"hgvs_p1": "I354T",
"hgvs_p3": "p.(Ile354Thr)",
"location": "exon 13 of 16 position 25 of 70",
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"canonical": true,
"gene_symbol": "BBS4",
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"ensembl_support_level": "1",
"ensembl_appris": "principal1",
"mane_select": "NM_033028.5",
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"uniprot_id": "Q96RK4"
},
{
"name": "ENST00000395205.2",
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"coding_impact": "missense",
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],
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"coding_location": "362 of 528",
"canonical": false,
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"mane_select": null,
"mane_plus": null,
"uniprot_id": "Q96RK4"
},
{
"name": "ENST00000539603.1",
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"coding_impact": "missense",
"function": [
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],
"hgvs": "c.1025T>C",
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"coding_location": "342 of 508",
"canonical": false,
"gene_symbol": "BBS4",
"splice_distance": "25",
"ensembl_support_level": null,
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"mane_select": null,
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"uniprot_id": null
},
{
"name": "ENST00000542334.1",
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"coding_impact": "missense",
"function": [
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],
"hgvs": "c.545T>C",
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"canonical": false,
"gene_symbol": "BBS4",
"splice_distance": "25",
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"mane_select": null,
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"uniprot_id": "Q96RK4"
},
{
"name": "ENST00000562084.1",
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"coding_impact": null,
"function": [
"non-coding exon"
],
"hgvs": null,
"hgvs_p1": null,
"hgvs_p3": null,
"location": "exon 13 of 16 position 25 of 70",
"coding_location": null,
"canonical": false,
"gene_symbol": "BBS4",
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"ensembl_support_level": "1",
"ensembl_appris": null,
"mane_select": null,
"mane_plus": null,
"uniprot_id": null
},
{
"name": "ENST00000562219.1",
"strand": "+",
"coding_impact": null,
"function": [
"non-coding exon"
],
"hgvs": null,
"hgvs_p1": null,
"hgvs_p3": null,
"location": "exon 5 of 5 position 25 of 533",
"coding_location": null,
"canonical": false,
"gene_symbol": "BBS4",
"splice_distance": "25",
"ensembl_support_level": "1",
"ensembl_appris": null,
"mane_select": null,
"mane_plus": null,
"uniprot_id": null
},
{
"name": "ENST00000566197.1",
"strand": "+",
"coding_impact": "missense",
"function": [
"coding"
],
"hgvs": "c.104T>C",
"hgvs_p1": "I35T",
"hgvs_p3": "p.(Ile35Thr)",
"location": "exon 2 of 5 position 61 of 106",
"coding_location": "35 of 179",
"canonical": false,
"gene_symbol": "BBS4",
"splice_distance": "-46",
"ensembl_support_level": "3",
"ensembl_appris": null,
"mane_select": null,
"mane_plus": null,
"uniprot_id": null
},
{
"name": "ENST00000566400.1",
"strand": "+",
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],
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"uniprot_id": null
},
{
"name": "ENST00000567279.1",
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"uniprot_id": null
},
{
"name": "ENST00000568535.1",
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"function": [
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],
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"location": "380 bp before transcription start site",
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"mane_select": null,
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},
{
"name": "ENST00000569151.1",
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}
],
"version": "112"
}
],
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"acmg_reannotated": "Benign",
"source": "UNIPROT UniProt Variants",
"codon": 354,
"gene_symbol": "BBS4",
"hgvs": "I354T",
"transcript": "NM_033028.5",
"pub_med_references": [
15666242,
15770229
],
"disease_name": [
"Bardet-Biedl syndrome",
"Bardet-Biedl syndrome 1",
"Bardet-Biedl syndrome 4"
],
"annotation_id": "VAR_017054"
}
]
}
}
]
}
],
"acmg_annotation": {
"version_name": "12.6.2",
"gene_symbol": "BBS4",
"transcript": "NM_033028.5",
"transcript_reason": "MANE select",
"coding_impact": "missense",
"blosum_score": -3,
"verdict": {
"ACMG_rules": {
"benign_score": 16,
"benign_subscore": "Benign",
"clinical_score": 1.234,
"pathogenic_score": 0,
"pathogenic_subscore": "Uncertain Significance",
"total_score": -16,
"verdict": "Benign"
},
"classifications": [
"BA1",
"BP4_Strong",
"BP6_Strong"
]
},
"classifications": [
{
"name": "BA1",
"met_criteria": true,
"user_explain": [
"GnomAD exomes allele frequency = 0.573 is greater than 0.05 threshold, good gnomAD exomes coverage = 75.8."
]
},
{
"name": "BP4",
"met_criteria": true,
"user_explain": [
"MetaRNN = 0.00000207 is less than 0.00692 ⇒ very strong benign."
],
"strength": "Strong"
},
{
"name": "BP6",
"met_criteria": true,
"user_explain": [
"Combined evidence strength is Strong (score = 5).",
"Strong: ClinVar classifies this variant as Benign, 2 stars (reviewed Nov '24, 11 submissions of which 1 is from high confidence submitter), citing %%PUBMED:12016587%%.",
"Supporting: UniProt Variants classifies this variant as Benign, citing 3 articles (%%PUBMED:15770229%%, %%PUBMED:15666242%% and %%PUBMED:14702039%%)."
],
"strength": "Strong"
}
],
"gene_id": 1959,
"sample_findings": {
"phenotypes": "No matching phenotype found for gene BBS4 which is associated with Bardet-Biedl Syndrome, Bardet-Biedl Syndrome 4, Bardet-Biedl Syndrome 4 615982, Bardet-Biedl Syndrome 4, 209900 and 9 more, according to CGD, ClinGen Disease Validity, GenCC, Mondo, PanelApp and gene2phenotype.",
"mode_of_inheritance": "AR, based on gene information from CGD, ClinGen Disease Validity, GenCC, Mondo, PanelApp and gene2phenotype."
}
},
"phylop100way": [
{
"version": "13-Apr-2021",
"conservation_score": [
"-0.245"
]
}
],
"maxentscan": null
}