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GeneBe

rs1799853

chr10-94942290-C-Achr10-94942290-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2_SupportingPM5PP3

The NM_000771(CYP2C9):c.430C>A(p.Arg144Ser) 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 pathogenic 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. R144C) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

CYP2C9
NM_000771 missense

Scores

1
5
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0520

Links

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
PM5
?
Other missense variant is known to change same aminoacid residue: Variant chr10-94942290-C-T is described in Lovd as [Pathogenic].
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.746

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP2C9NM_000771.4 linkuse as main transcriptc.430C>A p.Arg144Ser missense_variant 3/9 ENST00000260682.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP2C9ENST00000260682.8 linkuse as main transcriptc.430C>A p.Arg144Ser missense_variant 3/91 NM_000771.4 P1P11712-1

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Uncertain
0.029
T
BayesDel_noAF
Benign
-0.20
Cadd
Benign
19
Dann
Uncertain
1.0
Eigen
Benign
-0.10
Eigen_PC
Benign
-0.32
FATHMM_MKL
Benign
0.051
N
LIST_S2
Benign
0.43
T;T
M_CAP
Benign
0.037
D
MetaRNN
Pathogenic
0.75
D;D
MetaSVM
Uncertain
-0.26
T
MutationAssessor
Uncertain
2.8
M;M
MutationTaster
Benign
0.66
D
PrimateAI
Benign
0.31
T
Polyphen
1.0
.;D
Vest4
0.53
MutPred
0.57
Gain of phosphorylation at R144 (P = 0.0367);Gain of phosphorylation at R144 (P = 0.0367);
MVP
0.81
MPC
0.054
ClinPred
0.97
D
GERP RS
1.4
Varity_R
0.93
gMVP
0.25

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: chr10-96702047;