chr19-11105218-A-C

Variant names:

• chr19-11105218-A-C
• rs879254470
• NM_000527.5:c.314-2A>C

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_Strong PM2 PP5_Very_Strong

The NM_000527.5(LDLR):​c.314-2A>C variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.00000657 in 152,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
• Consequence: LDLR NM_000527.5 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10
• Conservation: PhyloP100: 4.63

Genes affected

LDLR (HGNC:6547): (low density lipoprotein receptor) The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. The encoded protein is normally bound at the cell membrane, where it binds low density lipoprotein/cholesterol and is taken into the cell. Lysosomes release the cholesterol, which is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.1475029 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-11105218-A-C is Pathogenic according to our data. Variant chr19-11105218-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 251142.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11105218-A-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDLR	NM_000527.5	c.314-2A>C		splice_acceptor_variant, intron_variant	Intron 3 of 17	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.314-2A>C		splice_acceptor_variant, intron_variant	Intron 3 of 17	1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152150 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 33

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152150 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74316

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:4

Nov 08, 2022

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 25, 2016

LDLR-LOVD, British Heart Foundation

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: literature only

- -

-

Robarts Research Institute, Western University

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 02, 2024

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.314-2A>C intronic variant, also known as IVS3-2A>C is located at the canonical acceptor splice site of intron 3 of the LDLR gene, that encodes for low density lipoprotein receptor. This variant has been reported in at least ten individuals affected with familial hypercholesterolemia (FH) (PMID:11668627, 27765764, 34037665, 32220565). Another intronic variant affecting the same nucleotide, c.314-2A>G, has also been reported in individuals with FH (PMID: 27824480). Variants affecting the same splice site (c.314-1G>A and c.314-3C>T) have been observed in individuals diagnosed with FH (PMID 11810272, 16250003). In-silico computational prediction tools suggest that the c.314-2A>C variant likely leads to acceptor loss (SpliceAI: 0.99 [acceptor loss], 0.32 [acceptor gain at +10bp position]) and disturb normal splicing, resulting in aberrant or absence of protein product (PMID: 16199547). This variant is absent in the general population database, gnomAD. This variant has been interpreted as likely pathogenic/pathogenic by multiple submitters in the ClinVar database (ID: 251142). Therefore, the c.314-2A>C intronic variant in the LDLR gene is classified as pathogenic. -

Familial hypercholesterolemia Pathogenic:3

Sep 05, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant (also known as IVS3-2A>C) causes an A to C nucleotide substitution at the -2 canonical splice acceptor site of intron 3 of the LDLR gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing. Although this prediction has not been confirmed in published RNA studies, this variant is expected to result in an absent or disrupted protein product. This variant has been reported in at least 8 individuals affected with familial hypercholesterolemia (PMID: 11668627, 27765764, 27824480, 32220565). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of LDLR function is a known mechanism of disease. Based on available evidence, this variant is classified as Likely Pathogenic. -

Oct 18, 2023

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.314-2A>C intronic variant, also known as IVS3-2A>C is located at the canonical acceptor splice site of intron 3 of the LDLR gene, that encodes for low density lipoprotein receptor. This variant has been reported in at least ten individuals affected with familial hypercholesterolemia (FH) (PMID:11668627, 27765764, 34037665, 32220565). Another intronic variant affecting the same nucleotide, c.314-2A>G, has also been reported in individuals with FH (PMID: 27824480). Variants affecting the same splice site (c.314-1G>A and c.314-3C>T) have been observed in individuals diagnosed with FH (PMID 11810272, 16250003). In-silico computational prediction tools suggest that the c.314-2A>C variant likely leads to acceptor loss (SpliceAI: 0.99 [acceptor loss], 0.32 [acceptor gain at +10bp position]) and disturb normal splicing, resulting in aberrant or absence of protein product (PMID: 16199547). This variant is absent in the general population database, gnomAD. This variant has been interpreted as likely pathogenic/pathogenic by multiple submitters in the ClinVar database (ID: 251142). Therefore, the c.314-2A>C intronic variant in the LDLR gene is classified as pathogenic. -

Sep 17, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects an acceptor splice site in intron 3 of the LDLR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 28645073). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with familial hypercholesterolemia (PMID: 27765764, 27824480). This variant is also known as IVS3-2A>C inthe literature. ClinVar contains an entry for this variant (Variation ID: 251142). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Homozygous familial hypercholesterolemia Pathogenic:1

Mar 21, 2018

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.314-2A>C variant in LDLR has been reported in the heterozygous state in at least 5 individuals with familial hypercholesterolemia (FH; Wang 2001, Wang 2016. This variant has also been reported in ClinVar (Variation ID: 251142) and was absent from large population studies. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing leading to the activation of a downstream splice site that would result in the first 8 bases of the exon to be spliced out, causing a frameshift which alters the protein's amino acid sequence and leads to a premature termination codon 22 amino acids downstream. In summary, although additional studies are required to fully establish its clinical significance, the c.314-2A>C variant is likely pathogenic. ACMG/AMP Criteria applied (Richards 2015): PVS1_Strong; PM2; PS4_Supporting. -

not provided Pathogenic:1

Jun 18, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 25525159, 27765764, 31447099, 32041611, 26582918, 32220565, 33303402, 11668627, 34037665) -

Cardiovascular phenotype Pathogenic:1

Feb 16, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.314-2A>C intronic pathogenic mutation results from an A to C substitution two nucleotides upstream from coding exon 4 in the LDLR gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown; however, the impacted region is critical for protein function (Ambry internal data). This alteration has been described in familial hypercholesterolemia (FH) cohorts (Wang J et al. Hum Mutat. 2001;18:359; Wang J et al. Arterioscler Thromb Vasc Biol, 2016 12;36:2439-2445; Sturm AC et al. JAMA Cardiol, 2021 08;6:902-909). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Another alteration impacting the same acceptor site (c.314-1G>A) has also been detected in individuals with FH (Huijgen et al 2010; Hum Mut 31(6):752-60; Lombardi P et al. Hum Mutat, 1998;Suppl 1:S172-4; Luirink IK et al. Atherosclerosis, 2019 06;285:87-92). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Benign	-0.090
CADD	Pathogenic	27
DANN	Uncertain	0.98
Eigen	Pathogenic	0.95
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Pathogenic	1.0	D
GERP RS		5.3
RBP_binding_hub_radar		0.67
RBP_regulation_power_radar		2.6

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.81
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.32		Position offset: 10
DS_AL_spliceai		0.99		Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs879254470; hg19: chr19-11215894;