11-63575024-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001128203.2(PLAAT3):c.410C>T(p.Ala137Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,612,598 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A137P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001128203.2 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 |
---|---|---|---|---|---|---|---|
PLAAT3 | NM_001128203.2 | c.410C>T | p.Ala137Val | missense_variant | 5/5 | ENST00000415826.3 | |
PLAAT3 | NM_007069.3 | c.410C>T | p.Ala137Val | missense_variant | 4/4 | ||
PLAAT3 | XM_011544741.2 | c.455C>T | p.Ala152Val | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAAT3 | ENST00000415826.3 | c.410C>T | p.Ala137Val | missense_variant | 5/5 | 2 | NM_001128203.2 | P1 | |
PLAAT3 | ENST00000323646.9 | c.410C>T | p.Ala137Val | missense_variant | 4/4 | 1 | P1 | ||
PLAAT3 | ENST00000394613.3 | n.504C>T | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000520 AC: 13AN: 249928Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135200
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1460230Hom.: 1 Cov.: 29 AF XY: 0.0000358 AC XY: 26AN XY: 726526
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152368Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.410C>T (p.A137V) alteration is located in exon 4 (coding exon 4) of the PLA2G16 gene. This alteration results from a C to T substitution at nucleotide position 410, causing the alanine (A) at amino acid position 137 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