The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000527.5(LDLR):c.1875C>T (p.Asn625=)

CA023600

68102 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: 7031c563-9112-4d59-afbf-40f361d8e6f6
Approved on: 2023-04-28
Published on: 2023-04-30

HGVS expressions

NM_000527.5:c.1875C>T
NM_000527.5(LDLR):c.1875C>T (p.Asn625=)
NC_000019.10:g.11120121C>T
CM000681.2:g.11120121C>T
NC_000019.9:g.11230797C>T
CM000681.1:g.11230797C>T
NC_000019.8:g.11091797C>T
NG_009060.1:g.35741C>T
ENST00000252444.10:c.2133C>T
ENST00000559340.2:c.1735C>T
ENST00000560467.2:c.1755C>T
ENST00000558518.6:c.1875C>T
ENST00000252444.9:c.2129C>T
ENST00000455727.6:c.1371C>T
ENST00000535915.5:c.1752C>T
ENST00000545707.5:c.1494C>T
ENST00000557933.5:c.1875C>T
ENST00000558013.5:c.1875C>T
ENST00000558518.5:c.1875C>T
ENST00000559340.1:c.456C>T
NM_000527.4:c.1875C>T
NM_001195798.1:c.1875C>T
NM_001195799.1:c.1752C>T
NM_001195800.1:c.1371C>T
NM_001195803.1:c.1494C>T
NM_001195798.2:c.1875C>T
NM_001195799.2:c.1752C>T
NM_001195800.2:c.1371C>T
NM_001195803.2:c.1494C>T
More

Likely Benign

Met criteria codes 4
BP4 BP2 BP7 PP1
Not Met criteria codes 19
BS2 BS1 BS4 BS3 BP3 PS1 PS2 PS3 PS4 BA1 PP3 PP4 PM6 PM2 PVS1 PM1 PM3 PM5 PM4

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.1875C>T (p.Asn625=) variant is classified as Likely Benign for Familial Hypercholesterolemia by applying evidence codes PP1, BP2, 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). Variant has 3 supporting evidence codes towards Benign, enough to classify as Likely benign, and only 1 supporting evidence codes towards Pathogenic. The Benign criteria overwhelms the Pathogenic criteria, so we are confident in classifying this variant as Likely benign. The supporting evidence is as follows: PP1: Variant segregates with FH phenotype in 2 informative meioses in 1 families from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. So PP1 is met. BP2: 1 individual from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge with LDLR c.1598G>A. Phenotype LDL 168mg/dl under statins - Htz phenotype, c.1598G>A - Pathogenic by these guidelines. BP4: No REVEL available, splicing evaluation needed. Functional data on splicing not available. A) variant not on limits. B) variant is exonic and at least 50bp upstream from the canonical donor site, but it does not create AG. C) there is an AG nearby. MES scores: variant cryptic = -1.41, wt cryptic = -2.30, canonical acceptor = 9.58. Ratio variant cryptic/wt cryptic: -1.41/-2.30 = 0.61 --- it is not above 1.1 Ratio variant cryptic/canonical acceptor: -1.41/9.58 = 0.15--- it is not above 0.9 Variant is not predicted to alter splicing. So BP4 is met. BP7: Variant is synonymous and meets BP4.
Met criteria codes
BP4
No REVEL available, splicing evaluation needed. Functional data on splicing not available. A) variant not on limits. B) variant is exonic and at least 50bp upstream from the canonical donor site, but it does not create AG. C) there is an AG nearby. MES scores: variant cryptic = -1.41, wt cryptic = -2.30, canonical acceptor = 9.58. Ratio variant cryptic/wt cryptic: -1.41/-2.30 = 0.61 --- it is not above 1.1 Ratio variant cryptic/canonical acceptor: -1.41/9.58 = 0.15--- it is not above 0.9 Variant is not predicted to alter splicing. So BP4 is met.
BP2
1 individual from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge with LDLR c.1598G>A. Phenotype LDL 168mg/dl under statins - Htz phenotype, c.1598G>A - Pathogenic by these guidelines.
BP7
Variant is synonymous and meets BP4.
PP1
Variant segregates with FH phenotype in 2 informative meioses in 1 families from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. So PP1 is met.
Not Met criteria codes
BS2
No data available
BS1
PopMax FAF = 0.0003355 ( 0.03355%)
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No in-frame deletions/insertions
PS1
The current variant is in a non-coding region.
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Variant doesn't meet PM2.
BA1
PopMax FAF = 0.0003355 ( 0.03355%)
PP3
No REVEL available, splicing evaluation needed. Functional data on splicing not available. A) variant not on limits. B) variant is exonic and at least 50bp upstream from the canonical donor site, but it does not create AG. C) there is an AG nearby. MES scores: variant cryptic = -1.41, wt cryptic = -2.30, canonical acceptor = 9.58. Ratio variant cryptic/wt cryptic: -1.41/-2.30 = 0.61 --- it is not above 1.1 Ratio variant cryptic/canonical acceptor: -1.41/9.58 = 0.15--- it is not above 0.9 Variant is not predicted to alter splicing.
PP4
Variant doesn't meet PM2.
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
PopMax MAF = 0.00059 (0.059%) in Latino (gnomAD v2.1.1).
PVS1
Not a null variant
PM1
Not on exon 4. Not a cysteine residue.
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
The current variant is in a non-coding region.
PM4
No in-frame deletions/insertions
Curation History
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