8-11802585-TCTTCCTAGTGTGAGCG-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_001287742.2(FDFT1):c.-75+131_-75+146delCTTCCTAGTGTGAGCG variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FDFT1
NM_001287742.2 intron
NM_001287742.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.98
Genes affected
FDFT1 (HGNC:3629): (farnesyl-diphosphate farnesyltransferase 1) This gene encodes a membrane-associated enzyme located at a branch point in the mevalonate pathway. The encoded protein is the first specific enzyme in cholesterol biosynthesis, catalyzing the dimerization of two molecules of farnesyl diphosphate in a two-step reaction to form squalene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 8-11802585-TCTTCCTAGTGTGAGCG-T is Pathogenic according to our data. Variant chr8-11802585-TCTTCCTAGTGTGAGCG-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 587362.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000421 AC: 2AN: 475182Hom.: 0 AF XY: 0.00000777 AC XY: 2AN XY: 257290
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2
AN:
475182
Hom.:
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AC XY:
2
AN XY:
257290
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Squalene synthase deficiency Pathogenic:2Other:1
May 29, 2018
Kids Research, The Children's Hospital at Westmead
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: research
- -
Oct 25, 2018
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only
- -
-
GeneReviews
Significance: not provided
Review Status: no classification provided
Collection Method: literature only
- -
Computational scores
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Calibrated prediction
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at