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GeneBe

rs2108622

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001082.5(CYP4F2):c.1297G>T(p.Val433Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V433M) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Consequence

CYP4F2
NM_001082.5 missense

Scores

7
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.68
Variant links:
Genes affected
CYP4F2 (HGNC:2645): (cytochrome P450 family 4 subfamily F member 2) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum. The enzyme starts the process of inactivating and degrading leukotriene B4, a potent mediator of inflammation. This gene is part of a cluster of cytochrome P450 genes on chromosome 19. Another member of this family, CYP4F11, is approximately 16 kb away. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3594392).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP4F2NM_001082.5 linkuse as main transcriptc.1297G>T p.Val433Leu missense_variant 11/13 ENST00000221700.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP4F2ENST00000221700.11 linkuse as main transcriptc.1297G>T p.Val433Leu missense_variant 11/131 NM_001082.5 P3P78329-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
41
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Benign
-0.025
T
BayesDel_noAF
Benign
-0.27
Cadd
Benign
20
Dann
Uncertain
0.99
DEOGEN2
Benign
0.078
T;.
Eigen
Benign
-0.16
Eigen_PC
Benign
-0.20
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Uncertain
0.90
D;D
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.36
T;T
MetaSVM
Benign
-0.58
T
MutationAssessor
Uncertain
2.2
M;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Benign
0.44
T
PROVEAN
Uncertain
-2.7
D;.
REVEL
Benign
0.14
Sift
Benign
0.040
D;.
Sift4G
Uncertain
0.055
T;T
Polyphen
0.54
P;.
Vest4
0.12
MutPred
0.44
Gain of relative solvent accessibility (P = 0.2751);Gain of relative solvent accessibility (P = 0.2751);
MVP
0.71
MPC
0.25
ClinPred
0.97
D
GERP RS
1.7
Varity_R
0.43
gMVP
0.79

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-15990431; API