3-39089294-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2

The NM_020839.4(WDR48):ā€‹c.1644A>Gā€‹(p.Gln548Gln) variant causes a synonymous change. The variant allele was found at a frequency of 0.000374 in 1,613,388 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 Likely benign (no stars).

Frequency

Genomes: š‘“ 0.00023 ( 0 hom., cov: 32)
Exomes š‘“: 0.00039 ( 0 hom. )

Consequence

WDR48
NM_020839.4 synonymous

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.62
Variant links:
Genes affected
WDR48 (HGNC:30914): (WD repeat domain 48) The protein encoded by this gene has been shown to interact with ubiquitin specific peptidase 1 (USP1), activating the deubiquitinating activity of USP1 and allowing it to remove the ubiquitin moiety from monoubiquitinated FANCD2. FANCD2 is ubiquitinated in response to DNA damage. [provided by RefSeq, Sep 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 3-39089294-A-G is Benign according to our data. Variant chr3-39089294-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3055098.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 35 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WDR48NM_020839.4 linkc.1644A>G p.Gln548Gln synonymous_variant 16/19 ENST00000302313.10 NP_065890.1 Q8TAF3-1A0A024R2L1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WDR48ENST00000302313.10 linkc.1644A>G p.Gln548Gln synonymous_variant 16/191 NM_020839.4 ENSP00000307491.5 Q8TAF3-1

Frequencies

GnomAD3 genomes
AF:
0.000230
AC:
35
AN:
152162
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000353
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000259
AC:
65
AN:
250738
Hom.:
0
AF XY:
0.000251
AC XY:
34
AN XY:
135536
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000878
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000537
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000389
AC:
568
AN:
1461108
Hom.:
0
Cov.:
30
AF XY:
0.000365
AC XY:
265
AN XY:
726842
show subpopulations
Gnomad4 AFR exome
AF:
0.000149
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000562
Gnomad4 NFE exome
AF:
0.000481
Gnomad4 OTH exome
AF:
0.000315
GnomAD4 genome
AF:
0.000230
AC:
35
AN:
152280
Hom.:
0
Cov.:
32
AF XY:
0.000215
AC XY:
16
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000353
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000294
Hom.:
0
Bravo
AF:
0.000238
EpiCase
AF:
0.000600
EpiControl
AF:
0.000356

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

WDR48-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesDec 29, 2022This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
8.4
DANN
Benign
0.85

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: rs142933874; hg19: chr3-39130785; API