Submissions for variant NM_000527.5(LDLR):c.2389+4A>G

dbSNP: rs758493597

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000237780	SCV001960943	uncertain significance	Hypercholesterolemia, familial, 1	2021-06-22	reviewed by expert panel	curation	NM_000527.5(LDLR):c.2389+4A>G variant is classified as variant of Uncertain significance for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3 and PP4) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: PM2 - PopMax MAF = 0.000008798 (0.0009%) in European non-Finnish (gnomAD v2.1.1). PP3 - No REVEL, splicing evaluation required. Functional data on splicing not available. A) variant located at -3 to +6 from canonical donor splice site Ratio variant/wt canonical acceptor/donor = 0,786004057 ---- It is below 0.8 PP4 - Variant meets PM2. Identified in 1 FH case from Ambry Genetics who fulfills Simon-Broome criteria.
LDLR-LOVD, British Heart Foundation	RCV000237780	SCV000295974	likely benign	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Fundacion Hipercolesterolemia Familiar	RCV000237780	SCV000607698	uncertain significance	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	research
Iberoamerican FH Network	RCV000237780	SCV000748157	uncertain significance	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	research
Labcorp Genetics (formerly Invitae), Labcorp	RCV000812185	SCV000952490	uncertain significance	Familial hypercholesterolemia	2018-10-04	criteria provided, single submitter	clinical testing	This sequence change falls in intron 16 of the LDLR gene. It does not directly change the encoded amino acid sequence of the LDLR protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs758493597, ExAC 0.002%). This variant has been observed in several individuals affected with familial hypercholesterolemia (PMID: 15241806). ClinVar contains an entry for this variant (Variation ID: 252304). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics	RCV002450747	SCV002737313	pathogenic	Cardiovascular phenotype	2021-04-09	criteria provided, single submitter	clinical testing	The c.2389+4A>G pathogenic mutation results from an A to G substitution 4 nucleotides after coding exon 16 in the LDLR gene. This variant has been identified in several cohorts of individuals with familial hypercholesterolemia in Spain; however, clinical information is limited (Alonso R et al. Clin. Biochem., 2009 Jun;42:899-903; Mozas P et al. Hum. Mutat., 2004 Aug;24:187; Bourbon M et al. Atherosclerosis, 2017 07;262:8-13; Ibarretxe D et al. Atherosclerosis, 2018 11;278:210-216). This variant co-segregated with disease in one family tested in our laboratory, and RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). The resulting transcript is in-frame and is not expected to trigger nonsense-mediated mRNA decay; however, the impacted region is critical for protein function (Ambry internal data). Other pathogenic alterations impacting the same donor site (c.2389G>T and c.2389+1G>T) have been shown to have a similar impact on splicing (Bourbon M et al. J. Med. Genet., 2009 May;46:352-7; Holla ØL et al. Mol. Genet. Metab., 2009 Apr;96:245-52). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000812185	SCV004222664	likely pathogenic	Familial hypercholesterolemia	2023-11-15	criteria provided, single submitter	clinical testing	Variant summary: LDLR c.2389+4A>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Four predict the variant weakens a 5' donor site. Four predict the variant creates a 3' acceptor site. Additionally, mRNA from carriers of this variant showed an additional band which PCR confirmed was lacking exon 16 (Aparicio_2023). The variant allele was found at a frequency of 4e-06 in 251356 control chromosomes. c.2389+4A>G has been reported in the literature in individuals affected with Familial Hypercholesterolemia in Spanish cohorts and registries, however these reports are lacking full clinical details of the individuals carrying the variant (Mozas_2004, Merino_2007, Alonso_2008, Martin-Campos_2018, Marco-Benedi_2022). However, a recent report showed that carriers of this variant have a high prevalence of familial history of premature ASCVD and hypercholesterolemia as well as significantly worse LDLc levels than the rest of the genetically confirmed FH cohort. In this cohort, a female carrier presented tendon xanthoma and a male carrier presented both corneal arcus and tendon xanthomas (Aparicio_2023). This last report provides strong evidence for causality. Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments. Four labs, including the ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel, classified the variant as VUS while one classified as likley benign and one classified as pathogenic. It is important to note, however, that all clinvar submitters have last updated their evidence prior to the recent report from Aparicio. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000237780	SCV000606636	benign	Hypercholesterolemia, familial, 1		no assertion criteria provided	research