rs104894363

chr12-110919160-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1 BP4_Strong BS2

The NM_000432.4(MYL2):c.37G>A(p.Ala13Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000222 in 1,613,650 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00022 (1 hom.)
• Consequence: MYL2 NM_000432.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:10 B:7 O:1
• Conservation: PhyloP100: 5.79

Genes affected

MYL2 (HGNC:7583): (myosin light chain 2) This gene encodes a major sarcomeric protein in mammalian striated muscle. The encoded protein plays a role in embryonic heart muscle structure and function, while phosphorylation of the encoded protein is involved in cardiac myosin cycling kinetics, torsion and function in adults. Mutations in this gene are associated with hypertrophic cardiomyopathy 10 and infant-onset myopathy. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 13 uncertain in NM_000432.4
• BP4: Computational evidence support a benign effect (MetaRNN=0.020629168).
• BS2: High AC in GnomAd at 31 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL2	NM_000432.4	c.37G>A	p.Ala13Thr	missense_variant	2/7	ENST00000228841.15
MYL2	NM_001406745.1	c.37G>A	p.Ala13Thr	missense_variant	2/6
MYL2	NM_001406916.1	c.-21G>A		5_prime_UTR_variant	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL2	ENST00000228841.15	c.37G>A	p.Ala13Thr	missense_variant	2/7	1	NM_000432.4	P1
MYL2	ENST00000548438.1	c.37G>A	p.Ala13Thr	missense_variant	2/6	3
MYL2	ENST00000546404.1	c.37G>A	p.Ala13Thr	missense_variant	2/2	2
MYL2	ENST00000663220.1	c.-21G>A		5_prime_UTR_variant	2/7

Frequencies

GnomAD3 genomes AF: 0.000204 AC: 31 AN: 152070 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000725

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000191

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000366 AC: 92 AN: 251380 Hom.: 0 AF XY: 0.000397 AC XY: 54 AN XY: 135862

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000578

Gnomad ASJ exome AF: 0.00546

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000654

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000237

Gnomad OTH exome AF: 0.000978

GnomAD4 exome AF: 0.000224 AC: 327 AN: 1461462 Hom.: 1 Cov.: 30 AF XY: 0.000232 AC XY: 169 AN XY: 726976

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00498

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000348

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000152

Gnomad4 OTH exome AF: 0.000364

GnomAD4 genome AF: 0.000204 AC: 31 AN: 152188 Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18 AN XY: 74422

Gnomad4 AFR AF: 0.0000722

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00403

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000191

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000357 Hom.: 0

Bravo AF: 0.000215

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000698 AC: 6

ExAC AF: 0.000305 AC: 37

EpiCase AF: 0.000218

EpiControl AF: 0.000237

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:10 Benign:7 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hypertrophic cardiomyopathy 10 Pathogenic:1 Uncertain:4 Benign:1 Other:1

not provided, no classification provided	curation	Leiden Muscular Dystrophy (MYL2)	Mar 26, 2012	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	Aug 25, 2020	- -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 28, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Clinical Genomics Program, Stanford Medicine	Jun 10, 2021	The p.Ala13Thr variant in the MYL2 gene has been previously reported in 3 unrelated individuals with hypertrophic cardiomyopathy and 1 unrelated asymptotic individual; this variant co-segregated with disease in at least 1 affected relative and failed to segregate with disease in at least 1 affected relative (Andersen et al., 2001; Ball et al., 2012; Li et al., 2017; Poetter et al., 1996). This variant has also been identified in 56/10,360 Ashkenazi Jewish and 29/129,136 European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This allele frequency is greater than would be expected to be disease-causing for hypertrophic cardiomyopathy. Functional studies of the p.Ala13Thr variant are supportive of a deleterious effect to the protein; however, it is unclear if this would be sufficient to be disease-causing (Kazmierczak et al., 2012). Computational tools predict that this variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Ala13Thr variant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PS3_supporting; PP3; BS1] -
Uncertain significance, criteria provided, single submitter	clinical testing	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	Nov 21, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Jan 27, 2016	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 01, 1996	- -

not provided Uncertain:3 Benign:2

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jun 28, 2022	The MYL2 c.37G>A; p.Ala13Thr variant (rs104894363) is reported in the literature in individuals and families affected with hypertrophic cardiomyopathy, but does not segregate with disease in all affected family members (Ball 2012, Hougs 2005, Klaassen 2008, Li 2017, Mook 2013). This variant is also reported in ClinVar (Variation ID: 14064), and is found in the Ashkenazi Jewish population with an allele frequency of 0.54% (56/10360 alleles) in the Genome Aggregation Database. The alanine at codon 13 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.532). Functional studies of the variant protein show this variant may affect contractile function and actin filament velocity in cardiac cells (Farman 2014, Roopnarine 2003, Szczesna 2001, Szczesna-Cordary 2004). Due to conflicting information, the clinical significance of this variant is uncertain at this time. References: Ball MP et al. A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):11920-7. PMID: 22797899. Farman GP, Muthu P, Kazmierczak K, Szczesna-Cordary D, Moore JR. Impact of familial hypertrophic cardiomyopathy-linked mutations in the NH2 terminus of the RLC on beta-myosin cross-bridge mechanics. J Appl Physiol (1985). 2014 Dec 15;117(12):1471-7. PMID: 25324513. Hougs L et al. One third of Danish hypertrophic cardiomyopathy patients with MYH7 mutations have mutations in MYH7 rod region. Eur J Hum Genet. 2005 Feb;13(2):161-5. PMID: 15483641. Klaassen S et al. Mutations in sarcomere protein genes in left ventricular noncompaction. Circulation. 2008 Jun 3;117(22):2893-901. PMID: 18506004. Li L et al. A Potential Oligogenic Etiology of Hypertrophic Cardiomyopathy: A Classic Single-Gene Disorder. Circ Res. 2017 Mar 31;120(7):1084-1090. PMID: 28223422. Mook OR et al. Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics. J Med Genet. 2013 Sep;50(9):614-26. PMID: 23785128. Roopnarine O. Mechanical defects of muscle fibers with myosin light chain mutants that cause cardiomyopathy. Biophys J. 2003 Apr;84(4):2440-9. PMID: 12668451. Szczesna D et al. Familial hypertrophic cardiomyopathy mutations in the regulatory light chains of myosin affect their structure, Ca2+ binding, and phosphorylation. J Biol Chem. 2001 Mar 9;276(10):7086-92. PMID: 11102452. Szczesna-Cordary D, Guzman G, Ng SS, Zhao J. Familial hypertrophic cardiomyopathy-linked alterations in Ca2+ binding of human cardiac myosin regulatory light chain affect cardiac muscle contraction. J Biol Chem. 2004 Jan 30;279(5):3535-42. PMID: 14594949. -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 04, 2019	The p.Ala13Thr variant in MYL2 has been reported in 6 individuals with HCM and segregated with disease in 3 affected relatives from 2 families (Poetter 1996, Andersen 2001, Hougs 2005, Klaassen 2008, Mook 2013, LMM data). However, 2 additional relatives with cardiomyopathy from 2 families did not carry the p.Ala13Thr variant (2 non-segregations; Andersen 2001, LMM data). It has also been identified in 0.05% (34/66444) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs104894363). Functional studies examining effects of this mutation on protein function were not conclusive (Szczesna 2001, Szczesna-Cordary 2004, Farman 2014). Transgenic mice with the p.Ala13Thr variant have left ventricular hypertrophy (Kazmierczak 2012). However, this study may not accurately represent biological function. In summary, due to conflicting information, the clinical significance of the p.Ala13Thr variant is uncertain. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 18, 2023	Did not segregate with HCM phenotype in one affected relative tested at GeneDx and segregation data in the literature is not definitive (Hougs et al., 2005; Klaassen et al., 2008; Li et al., 2017); Published functional studies demonstrate a damaging effect (Szczesna et al., 2001; Roopnarine et al., 2003; Szczesna-Cordary et al., 2004; Kazmierczak et al., 2012; Nagwekar et al., 2015); nevertheless, it is unclear how these studies may translate to a pathogenic role in human disease; In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 14594949, 23785128, 23299917, 26074085, 30605904, 24055113, 23861362, 25637381, 25333069, 11102452, 25324513, 11748309, 27153395, 26385864, 27084718, 28510043, 26664906, 28223422, 23197161, 24111713, 26272908, 28518168, 23365102, 28467684, 22958901, 25351510, 31019283, 18506004, 30706179, 33232181, 31980526, 15483641, 22091967, 22797899, 12668451, 8673105, 35653365) -

Primary familial hypertrophic cardiomyopathy Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	Jun 20, 2016	- -
Uncertain significance, no assertion criteria provided	research	CSER _CC_NCGL, University of Washington	Jun 01, 2014	- -

Cardiomyopathy Uncertain:1 Benign:1

Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 16, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Feb 11, 2022	- -

Hypertrophic cardiomyopathy Benign:1

Benign, criteria provided, single submitter

research

Biesecker Lab/Clinical Genomics Section, National Institutes of Health

Apr 05, 2018

- -

Cardiovascular phenotype Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 30, 2020

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Hypertrophic cardiomyopathy 1 Benign:1

Likely benign, criteria provided, single submitter

research

Agnes Ginges Centre for Molecular Cardiology, Centenary Institute

Aug 29, 2017

The MYL2 Ala13Thr variant has been identified in multiple unrelated cases of HCM (see references) and was absent in over 350 normal chromosomes (Poetter et al., 1996; Anderson et al., 2001). It is also observed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/) with an allele frequency of 0.03% (37 alleles). Evidence of MYL2 Ala13Thr segregation with disease has been weak. Li et al, (2017) describes a HCM family consisting of 3 affected family members, 3 variants were identified in the proband, including MYL2 Ala13Thr, but unlike the other 2 variants, it did not segregate to all 3 affected. Anderson et al. (2001) observed this variant in one HCM family: 3 carriers (2 affected, 1 clinically unaffected 10yr-old); 1 genotype-negative individual had left ventricular hypertrophy which may be due to hypertension and obesity. The disease in this same family was later suspected to be due to another variant (MYH7 Asn1327Lys) but this did not segregate in 1 clinically affected individual who met diagnostic criteria for HCM (Hougs et al., 2004). Additionally, MYL2 Ala13Thr was found not to segregate with disease in an additional HCM family identified by LMM, they harboured an MYBPC3 variant (Ball et al., 2012). Further, it failed to segregate in one LVNC family (Klassen S, et al., 2008). Two of the HCM families described above were Ashekenazi Jewish (Anderson et al., 2001; Ball et al., 2012), interestingly genome screening in 44 Ashkenazi Jewish centenarians identified MYL2 A13T in 2 people over the age of 94yrs, suggesting that this variant is a common polymorphism in this sub-population (Fraundenberg-Hua Y, et al., 2014). Functional studies including cell models suggest that MYL2 Ala13Thr may alter contractile function (Szczesna-Cordary D, et al., 2001; Roopnarine O, 2003; Szczesna-Cordary et al., 2004) and actin filament velocity (Farman GP, et al., 2014) in cardiac cells. A transgenic mouse model published by Kazmierczak et al., (2012) showed abnormal remodelling of the heart. However, it is noted that these studies may not accurately represent the biological system, in fact the amino acid at this position is not conserved in rats or mice. We have identified the MYL2 Ala13Thr variant in 2 HCM probands, both of North West European descent. Neither proband has a family history of HCM or sudden cardiac death. We note that additional variants have been identified in one proband which may contribute to the disease phenotype (MYH7 Asp1652Tyr; DSG2 Asp535Glu). Although there is reasonable supportive evidence for the pathogenicty of MYL2 Ala13Thr, based on the lack of segregation reported and a population frequency greater 0.02%, we classify this variant as "likely benign". -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
CardioboostCm	Uncertain	0.43
BayesDel_addAF	Benign	-0.087	T
BayesDel_noAF	Uncertain	-0.070
Cadd	Uncertain	23
Dann	Uncertain	0.98
DEOGEN2	Uncertain	0.64	D;.
Eigen	Benign	-0.089
Eigen_PC	Benign	-0.064
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.81	T;T
M_CAP	Benign	0.062	D
MetaRNN	Benign	0.021	T;T
MetaSVM	Benign	-0.56	T
MutationAssessor	Benign	0.83	L;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-2.1	N;N
REVEL	Uncertain	0.53
Sift	Benign	0.066	T;T
Sift4G	Benign	0.17	T;T
Polyphen		0.80	P;.
Vest4		0.45
MVP		0.89
MPC		0.38
ClinPred		0.083	T
GERP RS		3.2
Varity_R		0.22
gMVP		0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs104894363; hg19: chr12-111356964; COSMIC: COSV57407078; COSMIC: COSV57407078;