rs372649110
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000377.3(WAS):c.1299G>A(p.Ala433=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00134 in 1,203,318 control chromosomes in the GnomAD database, including 15 homozygotes. There are 876 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A433A) has been classified as Likely benign.
Frequency
Consequence
NM_000377.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WAS | NM_000377.3 | c.1299G>A | p.Ala433= | synonymous_variant | 10/12 | ENST00000376701.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WAS | ENST00000376701.5 | c.1299G>A | p.Ala433= | synonymous_variant | 10/12 | 1 | NM_000377.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000799 AC: 89AN: 111457Hom.: 1 Cov.: 23 AF XY: 0.00125 AC XY: 42AN XY: 33677
GnomAD3 exomes AF: 0.00303 AC: 499AN: 164688Hom.: 0 AF XY: 0.00474 AC XY: 269AN XY: 56796
GnomAD4 exome AF: 0.00140 AC: 1528AN: 1091813Hom.: 14 Cov.: 33 AF XY: 0.00232 AC XY: 834AN XY: 359569
GnomAD4 genome ? AF: 0.000798 AC: 89AN: 111505Hom.: 1 Cov.: 23 AF XY: 0.00125 AC XY: 42AN XY: 33735
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 06, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Wiskott-Aldrich syndrome;C1839163:Thrombocytopenia 1;C1845987:X-linked severe congenital neutropenia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Wiskott-Aldrich syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at