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Variant: NM_000527.5(LDLR):c.1186+5G>C

CA16602324

375809 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: 9c52c4b2-e6a3-4075-a906-c44a2531c2c5

HGVS expressions

NM_000527.5:c.1186+5G>C
NM_000527.5(LDLR):c.1186+5G>C
NC_000019.10:g.11111644G>C
CM000681.2:g.11111644G>C
NC_000019.9:g.11222320G>C
CM000681.1:g.11222320G>C
NC_000019.8:g.11083320G>C
NG_009060.1:g.27264G>C
ENST00000558518.6:c.1186+5G>C
ENST00000252444.9:n.1440+5G>C
ENST00000455727.6:c.682+5G>C
ENST00000535915.5:c.1063+5G>C
ENST00000545707.5:c.805+5G>C
ENST00000557933.5:c.1186+5G>C
ENST00000558013.5:c.1186+5G>C
ENST00000558518.5:c.1186+5G>C
ENST00000560173.1:n.185+5G>C
ENST00000560467.1:n.666+5G>C
NM_000527.4:c.1186+5G>C
NM_001195798.1:c.1186+5G>C
NM_001195799.1:c.1063+5G>C
NM_001195800.1:c.682+5G>C
NM_001195803.1:c.805+5G>C
NM_001195798.2:c.1186+5G>C
NM_001195799.2:c.1063+5G>C
NM_001195800.2:c.682+5G>C
NM_001195803.2:c.805+5G>C

Uncertain Significance

Met criteria codes 3
PP4 PP3 PM2

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.1186+5G>C variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PP4) 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: PM2: PopMaxMAF = 0.0000809 in African/African American population in gnomAD (gnomAD v2.1.1). The PopMax is African/African American for this variant. However the allele number at this position for 19-11222320-G-C is 2 / 8710, which is < 10,000 in total and only genome data is available. Exome data from a neighboring variant 19-11222323-C-T, allele number 15994, was used for PopMaxMAF calculation: PopMaxMAF = 2 / (15994 + 8710) = 0.0000809 in African/African American population PP3: Variant is located within canonical intron 8 donor motif, splicing prediction is performed using MES: Wild type canonical donor motif tggGTGAGC score = 7.23, Variant canonical donor motif tggGTGACC score = 0.50, Var Score/Wt Score Ratio = 0.0692 which is <0.8, therefore PP3 is met. Predicted impact for alternative splicing caused by this variant is also confirmed by SpliceAI. PP4: Variant meets PM2 and is identified in 1 index case who fulfil Simon Broome criteria for possible FH and DLCN score = 6 (PMID 32220565, Table 2), after alternative causes of high cholesterol were excluded, reported by Brown et al, 2020, from Johns Hopkins University, US. PS3 not met: Functional data is not available.
Met criteria codes
PP4
Variant meets PM2 and is identified in 1 index case who fulfil Simon Broome criteria for possible FH and DLCN score = 6 (PMID 32220565, Table 2), after alternative causes of high cholesterol were excluded, reported by Brown et al, 2020, from Johns Hopkins University, US.
PP3
Variant is located within canonical intron 8 donor motif, splicing prediction is performed using MES: Wild type canonical donor motif tggGTGAGC score = 7.23, Variant canonical donor motif tggGTGACC score = 0.50, Var Score/Wt Score Ratio = 0.0692 which is <0.8, therefore PP3 is met. Predicted impact for alternative splicing caused by this variant is also confirmed by SpliceAI.
PM2
PopMaxMAF = 0.0000809 in African/African American population in gnomAD (gnomAD v2.1.1). The PopMax is African/African American for this variant. However the allele number at this position for 19-11222320-G-C is 2 / 8710, which is < 10,000 in total and only genome data is available. Exome data from a neighboring variant 19-11222323-C-T, allele number 15994, was used for PopMaxMAF calculation: PopMaxMAF = 2 / (15994 + 8710) = 0.0000809 in African/African American population
Approved on: 2023-03-24
Published on: 2023-04-01
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