rs694353
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_007166.4(PICALM):āc.1770T>Gā(p.Ala590=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 1,539,134 control chromosomes in the GnomAD database, including 266,035 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A590A) has been classified as Benign.
Frequency
Consequence
NM_007166.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PICALM | NM_007166.4 | c.1770T>G | p.Ala590= | synonymous_variant | 17/20 | ENST00000393346.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PICALM | ENST00000393346.8 | c.1770T>G | p.Ala590= | synonymous_variant | 17/20 | 1 | NM_007166.4 |
Frequencies
GnomAD3 genomes AF: 0.593 AC: 90083AN: 151998Hom.: 26886 Cov.: 33
GnomAD3 exomes AF: 0.597 AC: 149489AN: 250604Hom.: 45108 AF XY: 0.597 AC XY: 80852AN XY: 135452
GnomAD4 exome AF: 0.584 AC: 810694AN: 1387018Hom.: 239128 Cov.: 23 AF XY: 0.587 AC XY: 407591AN XY: 694432
GnomAD4 genome AF: 0.593 AC: 90155AN: 152116Hom.: 26907 Cov.: 33 AF XY: 0.588 AC XY: 43744AN XY: 74360
ClinVar
Submissions by phenotype
PICALM-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at