8-11808296-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_004462.5(FDFT1):c.100-498C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 1,223,746 control chromosomes in the GnomAD database, including 259,937 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.58 ( 26997 hom., cov: 31)
Exomes 𝑓: 0.66 ( 232940 hom. )
Consequence
FDFT1
NM_004462.5 intron
NM_004462.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
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 Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 8-11808296-C-T is Benign according to our data. Variant chr8-11808296-C-T is described in ClinVar as [Benign]. Clinvar id is 3054358.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FDFT1 | NM_004462.5 | c.100-498C>T | intron_variant | ENST00000220584.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FDFT1 | ENST00000220584.9 | c.100-498C>T | intron_variant | 1 | NM_004462.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.581 AC: 88199AN: 151760Hom.: 26964 Cov.: 31
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GnomAD4 exome AF: 0.657 AC: 704153AN: 1071868Hom.: 232940 Cov.: 39 AF XY: 0.656 AC XY: 331916AN XY: 506062
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GnomAD4 genome AF: 0.581 AC: 88277AN: 151878Hom.: 26997 Cov.: 31 AF XY: 0.587 AC XY: 43538AN XY: 74232
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FDFT1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at