chr2-28906570-C-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The NM_015131.3(WDR43):ā€‹c.474C>Gā€‹(p.Cys158Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,611,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)
Exomes š‘“: 0.000036 ( 0 hom. )

Consequence

WDR43
NM_015131.3 missense

Scores

11
8

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.42
Variant links:
Genes affected
WDR43 (HGNC:28945): (WD repeat domain 43) Enables RNA binding activity. Involved in positive regulation of rRNA processing and positive regulation of transcription by RNA polymerase I. Located in fibrillar center. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.28306094).
BS2
High AC in GnomAdExome4 at 52 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WDR43NM_015131.3 linkuse as main transcriptc.474C>G p.Cys158Trp missense_variant 3/18 ENST00000407426.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WDR43ENST00000407426.8 linkuse as main transcriptc.474C>G p.Cys158Trp missense_variant 3/181 NM_015131.3 P1
WDR43ENST00000440983.1 linkuse as main transcriptc.207C>G p.Cys69Trp missense_variant 3/54
WDR43ENST00000296126.6 linkuse as main transcriptc.-70C>G 5_prime_UTR_variant 2/85

Frequencies

GnomAD3 genomes
AF:
0.00000659
AC:
1
AN:
151796
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000689
AC:
17
AN:
246596
Hom.:
0
AF XY:
0.0000897
AC XY:
12
AN XY:
133732
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000501
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000333
GnomAD4 exome
AF:
0.0000356
AC:
52
AN:
1459252
Hom.:
0
Cov.:
33
AF XY:
0.0000579
AC XY:
42
AN XY:
725824
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000607
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000659
AC:
1
AN:
151796
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74070
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378
ExAC
AF:
0.0000414
AC:
5
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

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 GeneticsAug 22, 2023The c.474C>G (p.C158W) alteration is located in exon 3 (coding exon 3) of the WDR43 gene. This alteration results from a C to G substitution at nucleotide position 474, causing the cysteine (C) at amino acid position 158 to be replaced by a tryptophan (W). 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
Uncertain
0.49
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.15
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.20
T;.
Eigen
Uncertain
0.19
Eigen_PC
Benign
0.16
FATHMM_MKL
Uncertain
0.84
D
LIST_S2
Uncertain
0.88
D;D
M_CAP
Uncertain
0.27
D
MetaRNN
Benign
0.28
T;T
MetaSVM
Uncertain
-0.020
T
MutationAssessor
Benign
0.81
L;.
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.69
T
PROVEAN
Uncertain
-2.5
N;D
REVEL
Benign
0.26
Sift
Uncertain
0.012
D;D
Sift4G
Uncertain
0.010
D;T
Polyphen
1.0
D;.
Vest4
0.54
MutPred
0.62
Gain of MoRF binding (P = 0.0075);.;
MVP
0.13
MPC
0.76
ClinPred
0.29
T
GERP RS
4.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.45
gMVP
0.65

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: rs778949130; hg19: chr2-29129436; API