rs1253889825

Variant summary

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

The NM_052950.4(WDFY2):​c.68C>A​(p.Ser23Tyr) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

WDFY2
NM_052950.4 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.64
Variant links:
Genes affected
WDFY2 (HGNC:20482): (WD repeat and FYVE domain containing 2) This gene encodes a protein that contains two WD domains and an FYVE zinc finger region. The function of this gene is unknown. An alternatively spliced transcript variant of this gene may exist. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

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=0.39121547).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WDFY2NM_052950.4 linkc.68C>A p.Ser23Tyr missense_variant Exon 1 of 12 ENST00000298125.7 NP_443182.1 Q96P53

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WDFY2ENST00000298125.7 linkc.68C>A p.Ser23Tyr missense_variant Exon 1 of 12 1 NM_052950.4 ENSP00000298125.4 Q96P53
WDFY2ENST00000612477.1 linkc.68C>A p.Ser23Tyr missense_variant Exon 1 of 2 2 ENSP00000482942.1 A0A087WZX3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
0.0079
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
21
DANN
Benign
0.89
DEOGEN2
Benign
0.0099
.;T
Eigen
Benign
0.0072
Eigen_PC
Benign
0.18
FATHMM_MKL
Benign
0.41
N
LIST_S2
Benign
0.83
T;T
M_CAP
Benign
0.063
D
MetaRNN
Benign
0.39
T;T
MetaSVM
Benign
-0.85
T
MutationAssessor
Benign
1.4
.;L
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-0.44
.;N
REVEL
Benign
0.16
Sift
Benign
1.0
.;T
Sift4G
Benign
0.19
T;T
Polyphen
0.14
.;B
Vest4
0.54
MutPred
0.63
Loss of disorder (P = 0.0084);Loss of disorder (P = 0.0084);
MVP
0.70
MPC
0.50
ClinPred
0.34
T
GERP RS
5.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.27
gMVP
0.49

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1253889825; hg19: chr13-52158891; API