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.1060+9C>T

CA031713

369861 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
Link to MONDO
UUID: 10f9c785-44ea-4cac-8d0a-82364761cc6a
Approved on: 2023-04-28
Published on: 2023-05-01

HGVS expressions

NM_000527.5:c.1060+9C>T
NM_000527.5(LDLR):c.1060+9C>T
NC_000019.10:g.11110780C>T
CM000681.2:g.11110780C>T
NC_000019.9:g.11221456C>T
CM000681.1:g.11221456C>T
NC_000019.8:g.11082456C>T
NG_009060.1:g.26400C>T
ENST00000558518.6:c.1060+9C>T
ENST00000252444.9:n.1314+9C>T
ENST00000455727.6:c.556+9C>T
ENST00000535915.5:c.937+9C>T
ENST00000545707.5:c.679+9C>T
ENST00000557933.5:c.1060+9C>T
ENST00000558013.5:c.1060+9C>T
ENST00000558518.5:c.1060+9C>T
ENST00000560173.1:n.59+9C>T
ENST00000560467.1:n.541-734C>T
NM_000527.4:c.1060+9C>T
NM_001195798.1:c.1060+9C>T
NM_001195799.1:c.937+9C>T
NM_001195800.1:c.556+9C>T
NM_001195803.1:c.679+9C>T
NM_001195798.2:c.1060+9C>T
NM_001195799.2:c.937+9C>T
NM_001195800.2:c.556+9C>T
NM_001195803.2:c.679+9C>T

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 21
BS4 BS3 BS1 BS2 BP7 BP2 PS2 PS4 PS3 PS1 BA1 PP4 PP1 PP3 PM6 PM2 PM3 PM1 PM4 PM5 PVS1

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.1060+9C>T variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence code 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: BP4: No Revel score. The variant does not affect splicing process, the variant is located out of range for all scenarios.
Met criteria codes
BP4
No Revel score. The variant does not affect splicing process, the variant is located out of range for all scenarios.
Not Met criteria codes
BS4
Not met.
BS3
No functional evidence.
BS1
FAF = 0.0001782 in East Asians, this is not between .002 and .005, so BA1 is not met.
BS2
Not met.
BP7
Not met.
BP2
Not met.
PS2
Not met.
PS4
Not met.
PS3
No functional evidence.
PS1
Not met.
BA1
FAF = 0.0001782 in East Asians, this is less than .005 so BA1 is not met.
PP4
Not met.
PP1
Not met.
PP3
No Revel score. The variant does not affect splicing process, the variant is located out of range for all scenarios.
PM6
Not met.
PM2
PopMax MAF = .00040, this is greater than .0002 so PM2 is not met.
PM3
Not met.
PM1
Not located in exon 4.
PM4
Not an in-frame deletion or insertion.
PM5
Not met.
PVS1
Not a null variant.
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