chr5-168292172-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_015238.3(WWC1):āc.20C>Gā(p.Pro7Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000042 in 1,546,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.000044 ( 0 hom. )
Consequence
WWC1
NM_015238.3 missense
NM_015238.3 missense
Scores
7
9
3
Clinical Significance
Conservation
PhyloP100: 4.42
Genes affected
WWC1 (HGNC:29435): (WW and C2 domain containing 1) The protein encoded by this gene is a cytoplasmic phosphoprotein that interacts with PRKC-zeta and dynein light chain-1. Alleles of this gene have been found that enhance memory in some individuals. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.822
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWC1 | NM_015238.3 | c.20C>G | p.Pro7Arg | missense_variant | 1/23 | ENST00000265293.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWC1 | ENST00000265293.9 | c.20C>G | p.Pro7Arg | missense_variant | 1/23 | 1 | NM_015238.3 | P1 | |
WWC1 | ENST00000521089.5 | c.20C>G | p.Pro7Arg | missense_variant | 1/23 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151906Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000135 AC: 2AN: 148566Hom.: 0 AF XY: 0.0000126 AC XY: 1AN XY: 79394
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GnomAD4 exome AF: 0.0000445 AC: 62AN: 1394452Hom.: 0 Cov.: 31 AF XY: 0.0000392 AC XY: 27AN XY: 687906
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 151906Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74182
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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 submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.20C>G (p.P7R) alteration is located in exon 1 (coding exon 1) of the WWC1 gene. This alteration results from a C to G substitution at nucleotide position 20, causing the proline (P) at amino acid position 7 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MutPred
Loss of glycosylation at P7 (P = 0.032);Loss of glycosylation at P7 (P = 0.032);
MVP
MPC
1.0
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at