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NC_000019.10:g.11089452G>A AND Hypercholesterolemia, familial, 1

Germline classification:
Uncertain significance (3 submissions)
Last evaluated:
Aug 29, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000495878.14

Allele description [Variation Report for NC_000019.10:g.11089452G>A]

NC_000019.10:g.11089452G>A

Genes:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
LDLR-AS1:LDLR antisense RNA 1 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NC_000019.10:g.11089452G>A
HGVS:
  • NC_000019.10:g.11089452G>A
  • NG_009060.1:g.5072G>A
  • NM_000527.4:c.-97G>A
  • NM_001195798.1:c.-97G>A
  • NM_001195799.1:c.-97G>A
  • NM_001195800.1:c.-97G>A
  • NM_001195803.1:c.-97G>A
  • LRG_274t1:c.-97G>A
  • LRG_274:g.5072G>A
  • NC_000019.9:g.11200128G>A
  • NC_000019.9:g.11200128G>A
  • NR_163945.1:n.208C>T
Links:
dbSNP: rs944580031
NCBI 1000 Genomes Browser:
rs944580031
Molecular consequence:
  • NR_163945.1:n.208C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Hypercholesterolemia, familial, 1
Synonyms:
LDL RECEPTOR DISORDER; Hyperlipoproteinemia Type IIa; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007750; MedGen: C0745103; Orphanet: 391665; OMIM: 143890

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000583620U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Mar 30, 2017) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002817121ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel
reviewed by expert panel

(ClinGen FH ACMG Specifications v1-2)		Uncertain significance
(Aug 29, 2022) 		germlinecuration

Citation Link,

SCV004829717All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely Benign
(Aug 8, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided108544not providedclinical testing, curation
not providedgermlineyes11not providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille, SCV000583620.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Dutch Lipid Clinic Scoring : Probable FH

Description

ACMG Guidelines: Likely Pathogenic (ii)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not provided1not provided

From ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel, SCV002817121.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_000527.4(LDLR):c.-97G>A is a LDLR-AS1 Non Coding Transcript Variant and is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes PM2 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 follow: PM2_Met : absent from controls in GnomAD (gnomAD v2.1.1). PP4_Met : 1 index case with Dutch lipid clinic network >=6 PS4_supporting: variant met PM2 and was found in 1 index case with Dutch lipid clinic network >=6 (sequenced by progenica) from M.Arca Lab and 1 patient from Lille University & CHRU Lille (ClinVar entry) with Dutch Lipid Clinic Scoring of Probable FH

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From All of Us Research Program, National Institutes of Health, SCV004829717.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided1not providednot providednot provided

Last Updated: Oct 13, 2024