chrX-152990391-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001184924.2(PNMA5):c.1208G>A(p.Gly403Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001184924.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNMA5 | ENST00000535214.6 | c.1208G>A | p.Gly403Glu | missense_variant | Exon 4 of 4 | 3 | NM_001184924.2 | ENSP00000445775.1 | ||
PNMA5 | ENST00000361887.5 | c.1208G>A | p.Gly403Glu | missense_variant | Exon 2 of 2 | 1 | ENSP00000354834.5 | |||
PNMA5 | ENST00000439251.3 | c.1208G>A | p.Gly403Glu | missense_variant | Exon 2 of 2 | 1 | ENSP00000388850.1 | |||
PNMA5 | ENST00000452693.5 | c.1208G>A | p.Gly403Glu | missense_variant | Exon 3 of 3 | 2 | ENSP00000392342.1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.