3-146196750-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000354952.7(PLSCR4):c.668C>T(p.Ala223Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,613,748 control chromosomes in the GnomAD database, including 1 homozygotes. 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
ENST00000354952.7 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLSCR4 | NM_020353.3 | c.668C>T | p.Ala223Val | missense_variant | 7/9 | ENST00000354952.7 | NP_065086.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLSCR4 | ENST00000354952.7 | c.668C>T | p.Ala223Val | missense_variant | 7/9 | 1 | NM_020353.3 | ENSP00000347038 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 250866Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135612
GnomAD4 exome AF: 0.000113 AC: 165AN: 1461620Hom.: 1 Cov.: 31 AF XY: 0.000165 AC XY: 120AN XY: 727124
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.668C>T (p.A223V) alteration is located in exon 7 (coding exon 6) of the PLSCR4 gene. This alteration results from a C to T substitution at nucleotide position 668, causing the alanine (A) at amino acid position 223 to be replaced by a valine (V). 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