The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000527.5(LDLR):c.818-2A>G

CA10585149

251471 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: 488c0bd6-5804-48b9-b4d4-f616c13a8901

HGVS expressions

NM_000527.5:c.818-2A>G
NM_000527.5(LDLR):c.818-2A>G
NC_000019.10:g.11107390A>G
CM000681.2:g.11107390A>G
NC_000019.9:g.11218066A>G
CM000681.1:g.11218066A>G
NC_000019.8:g.11079066A>G
NG_009060.1:g.23010A>G
ENST00000558518.6:c.818-2A>G
ENST00000252444.9:n.1072-2A>G
ENST00000455727.6:c.314-2A>G
ENST00000535915.5:c.695-2A>G
ENST00000545707.5:c.437-2A>G
ENST00000557933.5:c.818-2A>G
ENST00000558013.5:c.818-2A>G
ENST00000558518.5:c.818-2A>G
ENST00000558528.1:n.333-2A>G
ENST00000560467.1:n.418-2A>G
NM_000527.4:c.818-2A>G
NM_001195798.1:c.818-2A>G
NM_001195799.1:c.695-2A>G
NM_001195800.1:c.314-2A>G
NM_001195803.1:c.437-2A>G
NM_001195798.2:c.818-2A>G
NM_001195799.2:c.695-2A>G
NM_001195800.2:c.314-2A>G
NM_001195803.2:c.437-2A>G

Pathogenic

Met criteria codes 6
PP4 PM2 PP1_Moderate PS4_Supporting PVS1 PS3_Supporting
Not Met criteria codes 20
PP3 PP2 PM6 PM3 PM1 PM4 PM5 BA1 BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Familial Hypercholesterolemia Expert Panel Specifications to the ACMG/AMP Variant Classification Guidelines Version 1.1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.818-2A>G variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PVS1, PP1_Moderate, PM2, PP4, PS3_Supporting and PS4_Supporting) 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: PVS1 - variant is in +2 AG splice site and has been proven to result in retention of 10 nt of intron5, which lead to out of frame consequence: p.Val273Glufs*31, so PVS1 is met. PP1_moderate - variant segregates with FH phenotype in 5 informative meiosis from 2 families from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge - 3 relatives with the phenotype have the variant and 2 relatives without phenotype do not have the variant. PP1_Moderate is met. PM2 - This variant is absent from gnomAD (gnomAD v2.1.1). PP4 - variant meets PM2. Identified in 3 unrelated index cases who fulfill SB criteria from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. PP4 is met PS3_supporting - Level 3 FS: Medeiros et al., 2010 (PMID 20828696) - Htz patients' lymphocytes, RNA assays - results: Retention of 10 nt of intron5 (p.Val273Glufs*31) --- an aberrant transcript was identified, so PS3_Supporting is met PS4_supporting - variant meets PM2. Identified in 3 unrelated index cases who fulfill SB criteria from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. PS4_Supporting is met.
Met criteria codes
PP4
variant meets PM2. identified in 3 unrelated index cases who fulfill SB criteria from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. PP4 is met
PM2
This variant is absent from gnomAD (gnomAD v2.1.1).
PP1_Moderate
variant segregates with FH phenotype in 5 informative meiosis from 2 families from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge - 3 relatives with the phenotype have the variant and 2 relatives without phenotype do not have the variant. PP1_Moderate is met
PS4_Supporting
variant meets PM2. identified in 3 unrelated index cases who fulfill SB criteria from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. PS4_Supporting is met
PVS1
variant is in +2 AG splice site and has been proven to result in retention of 10 nt of intron5, which lead to out of frame consequence: p.Val273Glufs*31, so PVS1 is met
PS3_Supporting
Level 3 FS: Medeiros et al., 2010 (PMID 20828696) - Htz patients' lymphocytes, RNA assays - results: Retention of 10 nt of intron5 (p.Val273Glufs*31) --- an aberrant transcript was identified, so PS3_Supporting is met
Not Met criteria codes
PP3
variant meets PVS1, so not applicable
PP2
not applicable
PM6
no de novo occurence identified
PM3
no index case with homozygous phenotype
PM1
variant is intronic, so not applicable
PM4
variant is intronic, so not applicable
PM5
variant is intronic, so not applicable
BA1
This variant is absent from gnomAD (gnomAD v2.1.1).
BS2
not identified in normolipidemic individuals: 0/190 non-FH alleles from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. BS2 is not met
BS4
1 non-segregation: 1 relative with phenotype does not have the variant from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. not enough, BS4 is not met
BS3
Level 3 FS: Medeiros et al., 2010 (PMID 20828696) - Htz patients' lymphocytes, RNA assays - results: Retention of 10 nt of intron5 (p.Val273Glufs*31) --- an aberrant transcript was identified, so BS3_Supporting is not met
BS1
This variant is absent from gnomAD (gnomAD v2.1.1).
BP5
not applicable
BP7
variant is intronic, so not applicable
BP2
1 index case from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, with LDL = 334mg/dl also has LDLR c.806G>A - Likely benign by the FH VCEP, so BP2 is not met
BP3
not applicable
BP4
variant meets PVS1, so not applicable
BP1
not applicable
PS2
no de novo occurence identified
PS1
variant is intronic, so not applicable
Approved on: 2021-12-13
Published on: 2022-07-11
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