Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_002709.3(PPP1CB):c.27C>T (p.Asp9=)

CA1589147

774811 (ClinVar)

Gene: PPP1CB
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 372ec7af-a0f4-4cd4-a4af-430b1f2258ab
Approved on: 2024-09-17
Published on: 2024-10-01

HGVS expressions

NM_002709.3:c.27C>T
NM_002709.3(PPP1CB):c.27C>T (p.Asp9=)
NC_000002.12:g.28752151C>T
CM000664.2:g.28752151C>T
NC_000002.11:g.28975017C>T
CM000664.1:g.28975017C>T
NC_000002.10:g.28828521C>T
NG_052878.1:g.5404C>T
ENST00000418910.2:c.27C>T
ENST00000420282.6:c.27C>T
ENST00000427786.2:c.-33+331C>T
ENST00000441461.6:c.27C>T
ENST00000455580.6:c.-33+331C>T
ENST00000703171.1:c.27C>T
ENST00000703172.1:c.-127C>T
ENST00000703173.1:c.27C>T
ENST00000703174.1:c.27C>T
ENST00000703175.1:n.38C>T
ENST00000395366.3:c.27C>T
ENST00000296122.10:c.27C>T
ENST00000358506.6:c.27C>T
ENST00000395366.2:c.27C>T
ENST00000420282.5:c.27C>T
ENST00000427786.1:c.-33+331C>T
ENST00000441461.5:c.27C>T
ENST00000455580.5:c.-33+331C>T
ENST00000464273.1:n.141C>T
NM_002709.2:c.27C>T
NM_206876.1:c.27C>T
NM_206876.2:c.27C>T
More

Benign

Met criteria codes 3
BA1 BP4 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PPP1CB Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.27C>T (p.Asp9=) variant in PPP1CB is a synonymous (silent) variant that is not predicted by SpliceAI to impact splicing. In addition, it occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser (BP4, BP7). The highest population minor allele frequency in gnomAD v4 is 0.002280 (2698/1145756 alleles) in the European (non-Finnish) population, which is higher than the ClinGen RASopathy VCEP threshold (>0.0005) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as benign for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: BA1, BP4, BP7. (RASopathy VCEP specifications version 1.1; 9/17/24)
Met criteria codes
BA1
The highest population minor allele frequency in gnomAD v4 is 0.002280 (2698/1145756 alleles) in the European (non-Finnish) population, which is higher than the ClinGen RASopathy VCEP threshold (>0.0005) for BA1, and therefore meets this criterion.
BP4
This variant occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser
BP7
This variant occurs at a nucleotide that is not conserved as shown by UCSC Genome Browser, not predicted by SpliceAI to impact splicing
Curation History
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