chrX-48684427-A-AC
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The ENST00000376701.5(WAS):c.273+4_273+5insC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0163 in 1,193,093 control chromosomes in the GnomAD database, including 123 homozygotes. There are 6,039 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000376701.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WAS | NM_000377.3 | c.273+11dupC | intron_variant | ENST00000376701.5 | NP_000368.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0191 AC: 2046AN: 107099Hom.: 23 Cov.: 21 AF XY: 0.0162 AC XY: 491AN XY: 30277
GnomAD3 exomes AF: 0.0137 AC: 2214AN: 161608Hom.: 14 AF XY: 0.0123 AC XY: 638AN XY: 51748
GnomAD4 exome AF: 0.0160 AC: 17385AN: 1085953Hom.: 98 Cov.: 32 AF XY: 0.0157 AC XY: 5547AN XY: 353855
GnomAD4 genome AF: 0.0192 AC: 2057AN: 107140Hom.: 25 Cov.: 21 AF XY: 0.0162 AC XY: 492AN XY: 30328
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2024 | WAS: BS1, BS2 - |
Wiskott-Aldrich syndrome;C1839163:Thrombocytopenia 1;C1845987:X-linked severe congenital neutropenia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 03, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at