22-38123113-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BS2
The NM_003560.4(PLA2G6):c.1573G>A(p.Ala525Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000265 in 1,549,300 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_003560.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000702 AC: 11AN: 156742Hom.: 0 AF XY: 0.0000970 AC XY: 8AN XY: 82516
GnomAD4 exome AF: 0.0000286 AC: 40AN: 1397092Hom.: 2 Cov.: 32 AF XY: 0.0000450 AC XY: 31AN XY: 689084
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not provided Uncertain:1
Observed in the heterozygous state in an individual with Parkinson's disease who also had a homozygous variant in the PRKN gene (Kumar et al., 2020); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.A471T; This variant is associated with the following publications: (PMID: Kousi[thesis]2011, 32707456) -
Iron accumulation in brain Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at