7-29883967-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080529.3(WIPF3):c.473C>A(p.Ala158Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000717 in 1,395,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080529.3 missense
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 |
---|---|---|---|---|---|---|---|---|
WIPF3 | NM_001080529.3 | c.473C>A | p.Ala158Glu | missense_variant | Exon 5 of 9 | ENST00000242140.10 | NP_001073998.2 | |
WIPF3 | NM_001391973.1 | c.473C>A | p.Ala158Glu | missense_variant | Exon 5 of 8 | NP_001378902.1 | ||
WIPF3 | XM_017012522.2 | c.440C>A | p.Ala147Glu | missense_variant | Exon 4 of 8 | XP_016868011.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WIPF3 | ENST00000242140.10 | c.473C>A | p.Ala158Glu | missense_variant | Exon 5 of 9 | 5 | NM_001080529.3 | ENSP00000242140.6 | ||
WIPF3 | ENST00000409123.5 | c.473C>A | p.Ala158Glu | missense_variant | Exon 5 of 8 | 5 | ENSP00000386790.1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 7.17e-7 AC: 1AN: 1395522Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 688478
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.473C>A (p.A158E) alteration is located in exon 5 (coding exon 4) of the WIPF3 gene. This alteration results from a C to A substitution at nucleotide position 473, causing the alanine (A) at amino acid position 158 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at