13-26681265-C-G
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_006646.6(WASF3):āc.928C>Gā(p.Pro310Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00551 in 1,613,400 control chromosomes in the GnomAD database, including 40 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 (ā ā ).
Frequency
Genomes: š 0.0034 ( 0 hom., cov: 32)
Exomes š: 0.0057 ( 40 hom. )
Consequence
WASF3
NM_006646.6 missense
NM_006646.6 missense
Scores
1
1
17
Clinical Significance
Conservation
PhyloP100: 5.54
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 Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.007344365).
BP6
Variant 13-26681265-C-G is Benign according to our data. Variant chr13-26681265-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 776903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 515 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WASF3 | NM_006646.6 | c.928C>G | p.Pro310Ala | missense_variant | 8/10 | ENST00000335327.6 | NP_006637.2 | |
LOC107984597 | XR_001749798.2 | n.1802G>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WASF3 | ENST00000335327.6 | c.928C>G | p.Pro310Ala | missense_variant | 8/10 | 1 | NM_006646.6 | ENSP00000335055 | P3 | |
WASF3 | ENST00000361042.8 | c.919C>G | p.Pro307Ala | missense_variant | 8/10 | 1 | ENSP00000354325 | A1 | ||
WASF3 | ENST00000671038.1 | c.919C>G | p.Pro307Ala | missense_variant | 8/9 | ENSP00000499292 |
Frequencies
GnomAD3 genomes AF: 0.00338 AC: 515AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00363 AC: 888AN: 244360Hom.: 6 AF XY: 0.00361 AC XY: 481AN XY: 133350
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GnomAD4 exome AF: 0.00573 AC: 8369AN: 1461074Hom.: 40 Cov.: 34 AF XY: 0.00566 AC XY: 4114AN XY: 726808
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GnomAD4 genome AF: 0.00338 AC: 515AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.00317 AC XY: 236AN XY: 74478
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | WASF3: BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.16
.;B
Vest4
MVP
MPC
0.84
ClinPred
T
GERP RS
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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