10-122429908-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001974.4(PLEKHA1):c.1185C>G(p.Asp395Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,613,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001974.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHA1 | NM_001001974.4 | c.1185C>G | p.Asp395Glu | missense_variant | 12/12 | ENST00000368990.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHA1 | ENST00000368990.8 | c.1185C>G | p.Asp395Glu | missense_variant | 12/12 | 1 | NM_001001974.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000329 AC: 50AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250770Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135518
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461536Hom.: 0 Cov.: 34 AF XY: 0.0000261 AC XY: 19AN XY: 727060
GnomAD4 genome ? AF: 0.000329 AC: 50AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.000310 AC XY: 23AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 12, 2024 | The c.1185C>G (p.D395E) alteration is located in exon 12 (coding exon 11) of the PLEKHA1 gene. This alteration results from a C to G substitution at nucleotide position 1185, causing the aspartic acid (D) at amino acid position 395 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