3-146206740-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020353.3(PLSCR4):c.140C>T(p.Pro47Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 1,595,602 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_020353.3 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLSCR4 | NM_020353.3 | c.140C>T | p.Pro47Leu | missense_variant | 4/9 | ENST00000354952.7 | NP_065086.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLSCR4 | ENST00000354952.7 | c.140C>T | p.Pro47Leu | missense_variant | 4/9 | 1 | NM_020353.3 | ENSP00000347038 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000277 AC: 6AN: 216592Hom.: 0 AF XY: 0.0000258 AC XY: 3AN XY: 116498
GnomAD4 exome AF: 0.0000201 AC: 29AN: 1443412Hom.: 0 Cov.: 31 AF XY: 0.0000223 AC XY: 16AN XY: 716380
GnomAD4 genome AF: 0.000131 AC: 20AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2022 | The c.140C>T (p.P47L) alteration is located in exon 4 (coding exon 3) of the PLSCR4 gene. This alteration results from a C to T substitution at nucleotide position 140, causing the proline (P) at amino acid position 47 to be replaced by a leucine (L). 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