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GeneBe

rs2108622

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PM2_SupportingBP4

The NM_001082(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 Genomes 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 missense

Scores

7
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.68

Links

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
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 P2P78329-1

Frequencies

GnomAD3 genomes
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
23
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

Find out SpliceAI 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;