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

Variant: NM_000527.5(LDLR):c.941-39C>T

CA030745

251548 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
Link to MONDO
UUID: 5351ddc9-0256-4220-8700-82063ca5060f
Approved on: 2023-04-28
Published on: 2023-05-01

HGVS expressions

NM_000527.5:c.941-39C>T
NM_000527.5(LDLR):c.941-39C>T
NC_000019.10:g.11110613C>T
CM000681.2:g.11110613C>T
NC_000019.9:g.11221289C>T
CM000681.1:g.11221289C>T
NC_000019.8:g.11082289C>T
NG_009060.1:g.26233C>T
ENST00000558518.6:c.941-39C>T
ENST00000252444.9:n.1195-39C>T
ENST00000455727.6:c.437-39C>T
ENST00000535915.5:c.818-39C>T
ENST00000545707.5:c.560-39C>T
ENST00000557933.5:c.941-39C>T
ENST00000558013.5:c.941-39C>T
ENST00000558518.5:c.941-39C>T
ENST00000560467.1:n.541-901C>T
NM_000527.4:c.941-39C>T
NM_001195798.1:c.941-39C>T
NM_001195799.1:c.818-39C>T
NM_001195800.1:c.437-39C>T
NM_001195803.1:c.560-39C>T
NM_001195798.2:c.941-39C>T
NM_001195799.2:c.818-39C>T
NM_001195800.2:c.437-39C>T
NM_001195803.2:c.560-39C>T

Benign

Met criteria codes 2
BA1 BP4
Not Met criteria codes 20
PVS1 BS2 BS4 BS3 BS1 BP2 BP3 PS2 PS4 PS3 PS1 PP4 PP1 PP3 PM6 PM2 PM3 PM1 PM4 PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Familial Hypercholesterolemia Expert Panel Specifications to the ACMG/AMP Variant Classification Guidelines Version 1.2

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.941-39C>T variant is classified as Benign for Familial Hypercholesterolemia by applying evidence codes BA1 and BP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: BA1: FAF=0.005249 (0.5249%) in European (Non-Finnish) exomes (gnomAD v2.1.1). So BA1 is met. BP4: The variant is not predicted to affect the splicing process by SpliceAI. So, BP4 is met.
Met criteria codes
BA1
FAF=0.005249 (0.5249%) in European (Non-Finnish) exomes (gnomAD v2.1.1). So BA1 is met.
BP4
The variant is not predicted to affect the splicing process by SpliceAI. So, BP4 is met.
Not Met criteria codes
PVS1
Not a null variant
BS2
No data available
BS4
No data available
BS3
No data available
BS1
FAF=0.005249 (0.5249%) in European (Non-Finnish) exomes (gnomAD v2.1.1).
BP2
No other specific FH-associated variant mentioned.
BP3
No in-frame deletions/insertions
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Variant does not meet PM2
PS3
No data available
PS1
Intronic variant
PP4
Variant doesn't meet PM2.
PP1
1 relative has the variant and LDL>75th percentile (1 informative meiosis)
PP3
Intronic variant
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
PopMax FAF=0.005249 (0.5249%) in European (Non-Finnish) exomes (gnomAD v2.1.1).
PM3
No other specific FH-associated variant mentioned.
PM1
Intronic variant
PM4
No in-frame deletions/insertions
PM5
Intronic variant
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