chr2-174562554-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001375834.1(WIPF1):c.1505C>T(p.Pro502Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,614,070 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P502P) has been classified as Likely benign.
Frequency
Consequence
NM_001375834.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WIPF1 | NM_001375834.1 | c.1505C>T | p.Pro502Leu | missense_variant | 8/8 | ENST00000679041.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WIPF1 | ENST00000679041.1 | c.1505C>T | p.Pro502Leu | missense_variant | 8/8 | NM_001375834.1 | P3 | ||
ENST00000442996.1 | n.217+15077G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251046Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135714
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727232
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
Wiskott-Aldrich syndrome 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 28, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 1397338). This variant has not been reported in the literature in individuals affected with WIPF1-related conditions. This variant is present in population databases (rs770286102, gnomAD 0.01%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 502 of the WIPF1 protein (p.Pro502Leu). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at