8-11808709-G-GTCCCACTCCCACTCCCACTCCCACTCCCAC
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004462.5(FDFT1):c.100-75_100-46dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.00033 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00040 ( 4 hom. )
Consequence
FDFT1
NM_004462.5 intron
NM_004462.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.258
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 Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FDFT1 | NM_004462.5 | c.100-75_100-46dup | intron_variant | ENST00000220584.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FDFT1 | ENST00000220584.9 | c.100-75_100-46dup | intron_variant | 1 | NM_004462.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 49AN: 148922Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000401 AC: 548AN: 1366048Hom.: 4 Cov.: 0 AF XY: 0.000513 AC XY: 345AN XY: 672634
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GnomAD4 genome AF: 0.000329 AC: 49AN: 149034Hom.: 0 Cov.: 0 AF XY: 0.000385 AC XY: 28AN XY: 72636
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Squalene synthase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Mar 19, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at