rs753915750
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001375834.1(WIPF1):c.1380C>T(p.Ser460Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000551 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001375834.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WIPF1 | NM_001375834.1 | c.1380C>T | p.Ser460Ser | synonymous_variant | Exon 7 of 8 | ENST00000679041.1 | NP_001362763.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251444Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135898
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727234
GnomAD4 genome AF: 0.000243 AC: 37AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74376
ClinVar
Submissions by phenotype
Wiskott-Aldrich syndrome 2 Uncertain:1Benign:1
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This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 0.09% (36/41452) (https://gnomad.broadinstitute.org/variant/2-174567146-G-A?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:540145). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant is a silent variant and does not change the amino acid, reducing the probability that this variant is disease causing. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at