13-26665074-C-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The ENST00000335327.6(WASF3):c.180C>A(p.Asn60Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000137 in 1,461,828 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
WASF3
ENST00000335327.6 missense
ENST00000335327.6 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 3.66
Genes affected
WASF3 (HGNC:12734): (WASP family member 3) This gene encodes a member of the Wiskott-Aldrich syndrome protein family. The gene product is a protein that forms a multiprotein complex that links receptor kinases and actin. Binding to actin occurs through a C-terminal verprolin homology domain in all family members. The multiprotein complex serves to tranduce signals that involve changes in cell shape, motility or function. A pseudogene of this gene have been defined on chromosome 6. Alternative splicing results in multiple transcript variants [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 20 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WASF3 | NM_006646.6 | c.180C>A | p.Asn60Lys | missense_variant | 4/10 | ENST00000335327.6 | NP_006637.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WASF3 | ENST00000335327.6 | c.180C>A | p.Asn60Lys | missense_variant | 4/10 | 1 | NM_006646.6 | ENSP00000335055 | P3 | |
WASF3 | ENST00000361042.8 | c.180C>A | p.Asn60Lys | missense_variant | 4/10 | 1 | ENSP00000354325 | A1 | ||
WASF3 | ENST00000671038.1 | c.180C>A | p.Asn60Lys | missense_variant | 4/9 | ENSP00000499292 | ||||
WASF3 | ENST00000496788.1 | n.348C>A | non_coding_transcript_exon_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251420Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135882
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461828Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727214
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GnomAD4 genome Cov.: 33
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33
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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 16, 2021 | The c.180C>A (p.N60K) alteration is located in exon 1 (coding exon 1) of the WASF3 gene. This alteration results from a C to A substitution at nucleotide position 180, causing the asparagine (N) at amino acid position 60 to be replaced by a lysine (K). 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
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.58
.;P
Vest4
MutPred
Gain of ubiquitination at N60 (P = 0.0211);Gain of ubiquitination at N60 (P = 0.0211);
MVP
MPC
1.1
ClinPred
D
GERP RS
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