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]
Link to SEPIO compliant JSON-LD document
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC related information was provided by the message!
  • No CSPEC computer assertion could be determined for this classification!
  • See Evidence submitted by expert panel for details.

Variant: NM_000527.5(LDLR):c.1383C>T (p.Gly461=)

CA034080

251823 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
Link to MONDO
UUID: 8e39a7e8-704f-445e-8bac-ef601fb25b70
Approved on: 2024-07-02
Published on: 2024-09-13

HGVS expressions

NM_000527.5:c.1383C>T
NM_000527.5(LDLR):c.1383C>T (p.Gly461=)
NC_000019.10:g.11113559C>T
CM000681.2:g.11113559C>T
NC_000019.9:g.11224235C>T
CM000681.1:g.11224235C>T
NC_000019.8:g.11085235C>T
NG_009060.1:g.29179C>T
ENST00000252444.10:c.1641C>T
ENST00000559340.2:c.1383C>T
ENST00000560467.2:c.1263C>T
ENST00000558518.6:c.1383C>T
ENST00000252444.9:c.1637C>T
ENST00000455727.6:c.879C>T
ENST00000535915.5:c.1260C>T
ENST00000545707.5:c.1002C>T
ENST00000557933.5:c.1383C>T
ENST00000558013.5:c.1383C>T
ENST00000558518.5:c.1383C>T
ENST00000559340.1:c.104C>T
ENST00000560467.1:c.863C>T
NM_000527.4:c.1383C>T
NM_001195798.1:c.1383C>T
NM_001195799.1:c.1260C>T
NM_001195800.1:c.879C>T
NM_001195803.1:c.1002C>T
NM_001195798.2:c.1383C>T
NM_001195799.2:c.1260C>T
NM_001195800.2:c.879C>T
NM_001195803.2:c.1002C>T

Likely Benign

Met criteria codes 3
BP7 BP4 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.1383C>T (p.Gly461=) variant is classified as Likely Benign for Familial Hypercholesterolemia by applying evidence codes PM2, BP4 and BP7 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012) on 2 July 2024. The supporting evidence is as follows: PM2: PopMax MAF = 0.0001157 (0.01157%) in the Latino-admixed population exomes (gnomAD v2.1.1). BP4: No REVEL, splicing evaluation required: A) not on limits B) does not create GT. Variant is not predicted to alter splicing. BP7: Variant is synonymous and meets BP4. This variant has two supporting strength evidence codes towards Benign, enough to classify as Likely Benign, and only one moderate strength evidence code towards Pathogenic. VCEP consensus is that PM2 is not strong enough evidence to upgrade the classification of an otherwise Benign or Likely Benign variant.
Met criteria codes
BP7
Variant is synonymous and meets BP4.
BP4
No REVEL, splicing evaluation required: A) not on limits B) does not create GT Variant is not predicted to alter splicing. Meets BP4
PM2
PopMax MAF = 0.0001157 (0.01157%) in the Latino-admixed population exomes (gnomAD v2.1.1).
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