8-11808615-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001287750.2(FDFT1):​c.98C>T​(p.Thr33Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,390,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000073 ( 0 hom. )

Consequence

FDFT1
NM_001287750.2 missense

Scores

6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.286
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08075121).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FDFT1NM_004462.5 linkc.100-179C>T intron_variant Intron 1 of 7 ENST00000220584.9 NP_004453.3 P37268-1Q6IAX1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FDFT1ENST00000220584.9 linkc.100-179C>T intron_variant Intron 1 of 7 1 NM_004462.5 ENSP00000220584.4 P37268-1

Frequencies

GnomAD3 genomes
AF:
0.0000658
AC:
10
AN:
152018
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000727
AC:
9
AN:
1238594
Hom.:
0
Cov.:
62
AF XY:
0.0000100
AC XY:
6
AN XY:
599562
show subpopulations
Gnomad4 AFR exome
AF:
0.0000823
Gnomad4 AMR exome
AF:
0.0000670
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000332
Gnomad4 SAS exome
AF:
0.0000345
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000198
Gnomad4 OTH exome
AF:
0.0000196
GnomAD4 genome
AF:
0.0000658
AC:
10
AN:
152018
Hom.:
0
Cov.:
33
AF XY:
0.0000673
AC XY:
5
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.000193
Gnomad4 AMR
AF:
0.0000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
CADD
Benign
12
DANN
Benign
0.94
FATHMM_MKL
Benign
0.068
N
LIST_S2
Benign
0.40
T
MetaRNN
Benign
0.081
T
GERP RS
-1.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.6
gMVP
0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs186055179; hg19: chr8-11666124; API