chr3-146533512-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021105.3(PLSCR1):c.52C>A(p.Pro18Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,607,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021105.3 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 | UniProt |
---|---|---|---|---|---|---|---|
PLSCR1 | NM_021105.3 | c.52C>A | p.Pro18Thr | missense_variant | 3/9 | ENST00000342435.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLSCR1 | ENST00000342435.9 | c.52C>A | p.Pro18Thr | missense_variant | 3/9 | 1 | NM_021105.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151986Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251360Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135834
GnomAD4 exome AF: 0.000214 AC: 311AN: 1455566Hom.: 0 Cov.: 28 AF XY: 0.000206 AC XY: 149AN XY: 724160
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151986Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.52C>A (p.P18T) alteration is located in exon 3 (coding exon 2) of the PLSCR1 gene. This alteration results from a C to A substitution at nucleotide position 52, causing the proline (P) at amino acid position 18 to be replaced by a threonine (T). 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