NM_006663.4:c.2433G>A
Variant names:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_006663.4(PPP1R13L):c.2433G>A(p.Pro811Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,612,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
PPP1R13L
NM_006663.4 synonymous
NM_006663.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.998
Genes affected
PPP1R13L (HGNC:18838): (protein phosphatase 1 regulatory subunit 13 like) IASPP is one of the most evolutionarily conserved inhibitors of p53 (TP53; MIM 191170), whereas ASPP1 (MIM 606455) and ASPP2 (MIM 602143) are activators of p53.[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 19-45382542-C-T is Benign according to our data. Variant chr19-45382542-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3895177.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.998 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0000205 (30/1460486) while in subpopulation MID AF= 0.000347 (2/5762). AF 95% confidence interval is 0.000061. There are 0 homozygotes in gnomad4_exome. There are 18 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1R13L | NM_006663.4 | c.2433G>A | p.Pro811Pro | synonymous_variant | Exon 12 of 13 | ENST00000360957.10 | NP_006654.2 | |
PPP1R13L | NM_001142502.2 | c.2433G>A | p.Pro811Pro | synonymous_variant | Exon 12 of 13 | NP_001135974.1 | ||
PPP1R13L | XM_017026177.2 | c.2433G>A | p.Pro811Pro | synonymous_variant | Exon 13 of 14 | XP_016881666.1 | ||
PPP1R13L | XM_017026178.2 | c.2433G>A | p.Pro811Pro | synonymous_variant | Exon 13 of 14 | XP_016881667.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248078Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134558
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460486Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 726446
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Apr 09, 2025
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at