X-118395319-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_019045.5(WDR44):ā€‹c.1028A>Gā€‹(p.Asn343Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000639 in 1,095,277 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 23)
Exomes š‘“: 0.0000064 ( 0 hom. 1 hem. )

Consequence

WDR44
NM_019045.5 missense

Scores

1
5
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.11
Variant links:
Genes affected
WDR44 (HGNC:30512): (WD repeat domain 44) This gene encodes a protein that interacts with the small GTPase rab11. A similar protein in rat binds the GTP-containing active form of rab11. This protein may play a role in endosome recycling. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13802966).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WDR44NM_019045.5 linkuse as main transcriptc.1028A>G p.Asn343Ser missense_variant 6/20 ENST00000254029.8 NP_061918.3 Q5JSH3-1
WDR44NM_001184965.2 linkuse as main transcriptc.1028A>G p.Asn343Ser missense_variant 6/20 NP_001171894.1 Q5JSH3-2
WDR44NM_001184966.1 linkuse as main transcriptc.953A>G p.Asn318Ser missense_variant 5/18 NP_001171895.1 Q5JSH3-4
WDR44XM_011531353.4 linkuse as main transcriptc.953A>G p.Asn318Ser missense_variant 5/19 XP_011529655.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WDR44ENST00000254029.8 linkuse as main transcriptc.1028A>G p.Asn343Ser missense_variant 6/201 NM_019045.5 ENSP00000254029.3 Q5JSH3-1
WDR44ENST00000371825.7 linkuse as main transcriptc.1028A>G p.Asn343Ser missense_variant 6/201 ENSP00000360890.3 Q5JSH3-2
WDR44ENST00000371848.3 linkuse as main transcriptc.725A>G p.Asn242Ser missense_variant 3/181 ENSP00000360914.3 H7BY83
WDR44ENST00000371822.9 linkuse as main transcriptc.953A>G p.Asn318Ser missense_variant 5/182 ENSP00000360887.5 Q5JSH3-4

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD3 exomes
AF:
0.0000165
AC:
3
AN:
181375
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
65907
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000220
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000639
AC:
7
AN:
1095277
Hom.:
0
Cov.:
28
AF XY:
0.00000277
AC XY:
1
AN XY:
360773
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000232
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23
Bravo
AF:
0.00000756
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 15, 2023The c.1028A>G (p.N343S) alteration is located in exon 6 (coding exon 6) of the WDR44 gene. This alteration results from a A to G substitution at nucleotide position 1028, causing the asparagine (N) at amino acid position 343 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.39
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Benign
0.18
.;T;.
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.90
D;D;D
M_CAP
Uncertain
0.25
D
MetaRNN
Benign
0.14
T;T;T
MetaSVM
Benign
-0.76
T
MutationAssessor
Uncertain
2.0
.;M;M
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-0.90
N;N;N
REVEL
Benign
0.089
Sift
Benign
0.19
T;T;T
Sift4G
Benign
0.21
T;T;T
Polyphen
0.0, 0.0010
.;B;B
Vest4
0.38
MutPred
0.23
.;Gain of phosphorylation at N343 (P = 0.0046);Gain of phosphorylation at N343 (P = 0.0046);
MVP
0.50
MPC
0.16
ClinPred
0.23
T
GERP RS
5.5
Varity_R
0.29
gMVP
0.43

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: rs765761577; hg19: chrX-117529282; API