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

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.258
Variant links:
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]

Genome browser will be placed here

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
FDFT1NM_004462.5 linkuse as main transcriptc.100-75_100-46dup intron_variant ENST00000220584.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FDFT1ENST00000220584.9 linkuse as main transcriptc.100-75_100-46dup intron_variant 1 NM_004462.5 P1P37268-1

Frequencies

GnomAD3 genomes
AF:
0.000329
AC:
49
AN:
148922
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000398
Gnomad ASJ
AF:
0.00145
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00301
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00321
Gnomad NFE
AF:
0.000297
Gnomad OTH
AF:
0.00147
GnomAD4 exome
AF:
0.000401
AC:
548
AN:
1366048
Hom.:
4
Cov.:
0
AF XY:
0.000513
AC XY:
345
AN XY:
672634
show subpopulations
Gnomad4 AFR exome
AF:
0.0000318
Gnomad4 AMR exome
AF:
0.000569
Gnomad4 ASJ exome
AF:
0.000810
Gnomad4 EAS exome
AF:
0.000781
Gnomad4 SAS exome
AF:
0.00408
Gnomad4 FIN exome
AF:
0.0000251
Gnomad4 NFE exome
AF:
0.000128
Gnomad4 OTH exome
AF:
0.000491
GnomAD4 genome
AF:
0.000329
AC:
49
AN:
149034
Hom.:
0
Cov.:
0
AF XY:
0.000385
AC XY:
28
AN XY:
72636
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000398
Gnomad4 ASJ
AF:
0.00145
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00301
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000297
Gnomad4 OTH
AF:
0.00145

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 submitterclinical testingAl Jalila Children’s Genomics Center, Al Jalila Childrens Speciality HospitalMar 19, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs71711801; hg19: chr8-11666218; API