1-117933381-G-C

Variant summary

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

The NM_006784.3(WDR3):ā€‹c.62G>Cā€‹(p.Ser21Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000088 in 1,614,172 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000053 ( 0 hom., cov: 32)
Exomes š‘“: 0.000092 ( 2 hom. )

Consequence

WDR3
NM_006784.3 missense

Scores

2
6
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.40
Variant links:
Genes affected
WDR3 (HGNC:12755): (WD repeat domain 3) This gene encodes a nuclear protein containing 10 WD repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, which usually include a trp-asp at the C-terminal end. Proteins belonging to the WD repeat family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. [provided by RefSeq, Jul 2008]

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=0.2753317).
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WDR3NM_006784.3 linkuse as main transcriptc.62G>C p.Ser21Thr missense_variant 2/27 ENST00000349139.6 NP_006775.1 Q9UNX4Q5TDG3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WDR3ENST00000349139.6 linkuse as main transcriptc.62G>C p.Ser21Thr missense_variant 2/271 NM_006784.3 ENSP00000308179.4 Q9UNX4
WDR3ENST00000369441.7 linkuse as main transcriptc.62G>C p.Ser21Thr missense_variant 2/101 ENSP00000358449.3 Q6PDA5
WDR3ENST00000471680.1 linkuse as main transcriptn.244G>C non_coding_transcript_exon_variant 2/55
WDR3ENST00000487202.5 linkuse as main transcriptn.153G>C non_coding_transcript_exon_variant 2/63

Frequencies

GnomAD3 genomes
AF:
0.0000526
AC:
8
AN:
152164
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000636
AC:
16
AN:
251422
Hom.:
0
AF XY:
0.0000957
AC XY:
13
AN XY:
135892
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.000198
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000261
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000528
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000917
AC:
134
AN:
1461890
Hom.:
2
Cov.:
30
AF XY:
0.000116
AC XY:
84
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000344
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000371
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000782
Gnomad4 OTH exome
AF:
0.0000828
GnomAD4 genome
AF:
0.0000525
AC:
8
AN:
152282
Hom.:
0
Cov.:
32
AF XY:
0.0000940
AC XY:
7
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000302
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000659
AC:
8
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

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 GeneticsMay 23, 2023The c.62G>C (p.S21T) alteration is located in exon 2 (coding exon 1) of the WDR3 gene. This alteration results from a G to C substitution at nucleotide position 62, causing the serine (S) at amino acid position 21 to be replaced by a threonine (T). 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
-0.18
T
BayesDel_noAF
Benign
-0.20
CADD
Uncertain
23
DANN
Benign
0.94
DEOGEN2
Benign
0.051
T;T
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.52
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.87
D;T
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.28
T;T
MetaSVM
Benign
-0.89
T
MutationAssessor
Uncertain
2.1
.;M
PrimateAI
Uncertain
0.70
T
PROVEAN
Benign
-1.7
N;D
REVEL
Benign
0.23
Sift
Uncertain
0.0040
.;D
Sift4G
Pathogenic
0.0
D;T
Polyphen
0.78
.;P
Vest4
0.52
MVP
0.72
MPC
0.13
ClinPred
0.17
T
GERP RS
5.1
Varity_R
0.51
gMVP
0.45

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: rs374993298; hg19: chr1-118476004; API