rs1047643
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_004462.5(FDFT1):āc.21T>Cā(p.Leu7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,610,252 control chromosomes in the GnomAD database, including 22,999 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.19 ( 3583 hom., cov: 34)
Exomes š: 0.16 ( 19416 hom. )
Consequence
FDFT1
NM_004462.5 synonymous
NM_004462.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.36
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP7
?
Synonymous conserved (PhyloP=1.36 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FDFT1 | NM_004462.5 | c.21T>C | p.Leu7= | synonymous_variant | 1/8 | ENST00000220584.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FDFT1 | ENST00000220584.9 | c.21T>C | p.Leu7= | synonymous_variant | 1/8 | 1 | NM_004462.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.195 AC: 29606AN: 152180Hom.: 3579 Cov.: 34
GnomAD3 genomes
?
AF:
AC:
29606
AN:
152180
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.130 AC: 31689AN: 243426Hom.: 2571 AF XY: 0.128 AC XY: 16854AN XY: 132112
GnomAD3 exomes
AF:
AC:
31689
AN:
243426
Hom.:
AF XY:
AC XY:
16854
AN XY:
132112
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.156 AC: 227142AN: 1457954Hom.: 19416 Cov.: 33 AF XY: 0.153 AC XY: 111263AN XY: 725062
GnomAD4 exome
AF:
AC:
227142
AN:
1457954
Hom.:
Cov.:
33
AF XY:
AC XY:
111263
AN XY:
725062
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.195 AC: 29641AN: 152298Hom.: 3583 Cov.: 34 AF XY: 0.185 AC XY: 13813AN XY: 74470
GnomAD4 genome
?
AF:
AC:
29641
AN:
152298
Hom.:
Cov.:
34
AF XY:
AC XY:
13813
AN XY:
74470
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
270
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at