rs35923393
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001375834.1(WIPF1):āc.78T>Cā(p.Asn26=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,613,924 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0017 ( 0 hom., cov: 32)
Exomes š: 0.0022 ( 7 hom. )
Consequence
WIPF1
NM_001375834.1 synonymous
NM_001375834.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.84
Genes affected
WIPF1 (HGNC:12736): (WAS/WASL interacting protein family member 1) This gene encodes a protein that plays an important role in the organization of the actin cytoskeleton. The encoded protein binds to a region of Wiskott-Aldrich syndrome protein that is frequently mutated in Wiskott-Aldrich syndrome, an X-linked recessive disorder. Impairment of the interaction between these two proteins may contribute to the disease. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 2-174581413-A-G is Benign according to our data. Variant chr2-174581413-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 472923.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-174581413-A-G is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=1.85 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WIPF1 | NM_001375834.1 | c.78T>C | p.Asn26= | synonymous_variant | 3/8 | ENST00000679041.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WIPF1 | ENST00000679041.1 | c.78T>C | p.Asn26= | synonymous_variant | 3/8 | NM_001375834.1 | P3 | ||
ENST00000442996.1 | n.217+33936A>G | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000454203.1 | n.203+5984A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00174 AC: 265AN: 152098Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00185 AC: 466AN: 251400Hom.: 0 AF XY: 0.00199 AC XY: 271AN XY: 135878
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GnomAD4 exome AF: 0.00221 AC: 3226AN: 1461708Hom.: 7 Cov.: 30 AF XY: 0.00219 AC XY: 1595AN XY: 727152
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GnomAD4 genome ? AF: 0.00174 AC: 265AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74420
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Wiskott-Aldrich syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
WIPF1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 14, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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