8-11808296-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.32
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 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
FDFT1NM_004462.5 linkuse as main transcriptc.100-498C>T intron_variant ENST00000220584.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FDFT1ENST00000220584.9 linkuse as main transcriptc.100-498C>T intron_variant 1 NM_004462.5 P1P37268-1

Frequencies

GnomAD3 genomes
AF:
0.581
AC:
88199
AN:
151760
Hom.:
26964
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.672
Gnomad AMR
AF:
0.666
Gnomad ASJ
AF:
0.551
Gnomad EAS
AF:
0.673
Gnomad SAS
AF:
0.720
Gnomad FIN
AF:
0.688
Gnomad MID
AF:
0.516
Gnomad NFE
AF:
0.661
Gnomad OTH
AF:
0.589
GnomAD4 exome
AF:
0.657
AC:
704153
AN:
1071868
Hom.:
232940
Cov.:
39
AF XY:
0.656
AC XY:
331916
AN XY:
506062
show subpopulations
Gnomad4 AFR exome
AF:
0.347
Gnomad4 AMR exome
AF:
0.680
Gnomad4 ASJ exome
AF:
0.557
Gnomad4 EAS exome
AF:
0.708
Gnomad4 SAS exome
AF:
0.695
Gnomad4 FIN exome
AF:
0.671
Gnomad4 NFE exome
AF:
0.665
Gnomad4 OTH exome
AF:
0.635
GnomAD4 genome
AF:
0.581
AC:
88277
AN:
151878
Hom.:
26997
Cov.:
31
AF XY:
0.587
AC XY:
43538
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.365
Gnomad4 AMR
AF:
0.667
Gnomad4 ASJ
AF:
0.551
Gnomad4 EAS
AF:
0.673
Gnomad4 SAS
AF:
0.719
Gnomad4 FIN
AF:
0.688
Gnomad4 NFE
AF:
0.661
Gnomad4 OTH
AF:
0.594
Alfa
AF:
0.606
Hom.:
3626
Bravo
AF:
0.570
Asia WGS
AF:
0.701
AC:
2441
AN:
3478

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 submitterclinical testingPreventionGenetics, part of Exact SciencesNov 25, 2020This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
2.1
DANN
Benign
0.92

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1736070; hg19: chr8-11665805; API