chr12-118043202-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_018639.5(WSB2):​c.358G>A​(p.Asp120Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0039 in 1,614,234 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0040 ( 28 hom. )

Consequence

WSB2
NM_018639.5 missense

Scores

3
16

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.89
Variant links:
Genes affected
WSB2 (HGNC:19222): (WD repeat and SOCS box containing 2) This gene encodes a member of the WD-protein subfamily. The encoded protein contains five WD-repeats spanning most of the protein and an SOCS box in the C-terminus. The SOCS box may act as a bridge between specific substrate-binding domains and E3 ubiquitin protein ligases. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0037802756).
BP6
Variant 12-118043202-C-T is Benign according to our data. Variant chr12-118043202-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643380.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00396 (5792/1461894) while in subpopulation MID AF= 0.0182 (105/5768). AF 95% confidence interval is 0.0154. There are 28 homozygotes in gnomad4_exome. There are 2948 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 28 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WSB2NM_018639.5 linkc.358G>A p.Asp120Asn missense_variant Exon 3 of 9 ENST00000315436.8 NP_061109.1 Q9NYS7-1
WSB2NM_001278557.1 linkc.409G>A p.Asp137Asn missense_variant Exon 3 of 9 NP_001265486.1 Q9NYS7-2
WSB2NM_001278558.2 linkc.-71-4814G>A intron_variant Intron 2 of 6 NP_001265487.1 Q9NYS7-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WSB2ENST00000315436.8 linkc.358G>A p.Asp120Asn missense_variant Exon 3 of 9 1 NM_018639.5 ENSP00000319474.3 Q9NYS7-1

Frequencies

GnomAD3 genomes
AF:
0.00328
AC:
499
AN:
152222
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000868
Gnomad AMI
AF:
0.0175
Gnomad AMR
AF:
0.00340
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00496
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.00494
Gnomad OTH
AF:
0.00860
GnomAD3 exomes
AF:
0.00358
AC:
900
AN:
251218
Hom.:
5
AF XY:
0.00410
AC XY:
557
AN XY:
135794
show subpopulations
Gnomad AFR exome
AF:
0.00105
Gnomad AMR exome
AF:
0.00185
Gnomad ASJ exome
AF:
0.00149
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00402
Gnomad FIN exome
AF:
0.000601
Gnomad NFE exome
AF:
0.00559
Gnomad OTH exome
AF:
0.00554
GnomAD4 exome
AF:
0.00396
AC:
5792
AN:
1461894
Hom.:
28
Cov.:
32
AF XY:
0.00405
AC XY:
2948
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.00108
Gnomad4 AMR exome
AF:
0.00241
Gnomad4 ASJ exome
AF:
0.00142
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00464
Gnomad4 FIN exome
AF:
0.000374
Gnomad4 NFE exome
AF:
0.00434
Gnomad4 OTH exome
AF:
0.00435
GnomAD4 genome
AF:
0.00326
AC:
496
AN:
152340
Hom.:
1
Cov.:
32
AF XY:
0.00313
AC XY:
233
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.000866
Gnomad4 AMR
AF:
0.00340
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00497
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.00494
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.00422
Hom.:
2
Bravo
AF:
0.00332
TwinsUK
AF:
0.00243
AC:
9
ALSPAC
AF:
0.00441
AC:
17
ESP6500AA
AF:
0.00113
AC:
5
ESP6500EA
AF:
0.00442
AC:
38
ExAC
AF:
0.00382
AC:
464
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.00769
EpiControl
AF:
0.00901

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2023WSB2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Benign
-0.48
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0040
T;.;.;.
Eigen
Benign
-0.30
Eigen_PC
Benign
-0.10
FATHMM_MKL
Benign
0.33
N
LIST_S2
Uncertain
0.88
D;D;D;D
M_CAP
Benign
0.0067
T
MetaRNN
Benign
0.0038
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.69
N;.;.;.
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-0.16
N;N;N;N
REVEL
Benign
0.070
Sift
Benign
0.25
T;T;T;T
Sift4G
Benign
0.49
T;T;T;.
Polyphen
0.0010
B;.;.;.
Vest4
0.23
MVP
0.10
MPC
0.60
ClinPred
0.027
T
GERP RS
5.1
Varity_R
0.045
gMVP
0.24

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: rs113350351; hg19: chr12-118481007; COSMIC: COSV59573495; COSMIC: COSV59573495; API