chr2-179945259-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_020943.3(CWC22):​c.2597G>A​(p.Ser866Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000583 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00029 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000034 ( 0 hom. )

Consequence

CWC22
NM_020943.3 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.44
Variant links:
Genes affected
CWC22 (HGNC:29322): (CWC22 spliceosome associated protein homolog) Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in cytosol and nuclear speck. Part of U2-type catalytic step 1 spliceosome; U2-type catalytic step 2 spliceosome; and U2-type precatalytic spliceosome. [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 -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0106651485).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CWC22NM_020943.3 linkc.2597G>A p.Ser866Asn missense_variant Exon 20 of 20 ENST00000410053.8 NP_065994.1 Q9HCG8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CWC22ENST00000410053.8 linkc.2597G>A p.Ser866Asn missense_variant Exon 20 of 20 1 NM_020943.3 ENSP00000387006.3 Q9HCG8

Frequencies

GnomAD3 genomes
AF:
0.000289
AC:
44
AN:
152140
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00104
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000926
AC:
23
AN:
248506
Hom.:
0
AF XY:
0.0000816
AC XY:
11
AN XY:
134800
show subpopulations
Gnomad AFR exome
AF:
0.00116
Gnomad AMR exome
AF:
0.0000870
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000890
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000342
AC:
50
AN:
1461466
Hom.:
0
Cov.:
31
AF XY:
0.0000261
AC XY:
19
AN XY:
726994
show subpopulations
Gnomad4 AFR exome
AF:
0.000986
Gnomad4 AMR exome
AF:
0.0000894
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000540
Gnomad4 OTH exome
AF:
0.0000994
GnomAD4 genome
AF:
0.000289
AC:
44
AN:
152258
Hom.:
0
Cov.:
33
AF XY:
0.000363
AC XY:
27
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.00104
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000695
Hom.:
0
Bravo
AF:
0.000461
ESP6500AA
AF:
0.00136
AC:
5
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000993
AC:
12

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Jan 16, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.2597G>A (p.S866N) alteration is located in exon 20 (coding exon 19) of the CWC22 gene. This alteration results from a G to A substitution at nucleotide position 2597, causing the serine (S) at amino acid position 866 to be replaced by an asparagine (N). 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
0.066
BayesDel_addAF
Benign
-0.64
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
19
DANN
Benign
0.94
DEOGEN2
Benign
0.019
T
Eigen
Benign
-0.31
Eigen_PC
Benign
-0.21
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.71
T
M_CAP
Benign
0.0064
T
MetaRNN
Benign
0.011
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.0
M
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-0.49
N
REVEL
Benign
0.063
Sift
Benign
0.41
T
Sift4G
Benign
0.47
T
Polyphen
0.18
B
Vest4
0.094
MVP
0.14
MPC
0.097
ClinPred
0.014
T
GERP RS
4.3
Varity_R
0.053
gMVP
0.031

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: rs190476525; hg19: chr2-180809986; API