rs200234935

chr20-31831697-C-Achr20-31831697-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_033118.4(MYLK2):c.1425-6C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYLK2 NM_033118.4 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.0004082
• Clinical Significance: Uncertain significance criteria provided, single submitter U:2
• Conservation: PhyloP100: 0.876

Genes affected

MYLK2 (HGNC:16243): (myosin light chain kinase 2) This gene encodes a myosin light chain kinase, a calcium/calmodulin dependent enzyme, that is exclusively expressed in adult skeletal muscle. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYLK2	NM_033118.4	c.1425-6C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000375985.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYLK2	ENST00000375985.5	c.1425-6C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_033118.4	P1
MYLK2	ENST00000375994.6	c.1425-6C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		P1
MYLK2	ENST00000468730.1	n.363-6C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, no assertion criteria provided

provider interpretation

Stanford Center for Inherited Cardiovascular Disease, Stanford University

Jan 24, 2018

c.1425-6C>A (IVS10-6C>A; Intronic) in the MYLK2 gene (NM_033118.3) Chromosome position: 20:30419500 C / A Based on the information reviewed below, we classify this as a Variant of Uncertain Significance (VUS), concluding that there is not sufficient evidence for its pathogenicity to warrant using it for predictive genetic testing. It is absent from population databases, but the only evidence currently pointing to pathogenicity comes from computer algorithms developed to predict splice site disruption. This variant has not been reported in the literature in individuals with MYLK2-related disease, according to the Invitae report. This is a variant in Intron 10 of 12. Invitae reports that 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 ExAC, Daniel MacArthur’s group from the Broad Institute has created a “constraint metric” for loss of function, indicating how tolerant each gene appears to be to heterozygous variants that lead to nonsense, splice acceptor, and splice donor variants that dramatically alter the protein. They call this pLI (Probability of LoF Intolerance). The closer the pLI is to 1, the more intolerant the gene appears to be. The pLI for the MYLK2 gene is 0.22, meaning that it appears to be fairly tolerant of heterozygous loss-of-function variants. Furthermore, this is a gene with only preliminary evidence currently associating it with hypertrophic cardiomyopathy—and not much is known about the type of variants that may prove to be disease causing. Of the 5 variants reported as Likely Pathogenic or Pathogenic to ClinVar by OMIM or a testing lab for MYLK2, 4 are missense and 1 is truncating. This variant is absent from the gnomAD database, which includes variant calls on ~140,000 individuals of European, African, Latino, South Asian, Ashkenazi, and East Asian descent. (Our patient’s ancestry is African-American and Caucasian.) There are 2 non-Finnish European ancestry individuals in gnomAD with a different nucleotide change at this same location: c.1425-6C>T. (Across ~90 vertebrate species for which we have data, ~16 have a T at this location, one has a G, and none have an A at this location like our patient does.) There is good sequencing coverage in gnomAD at this site. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. The curators made an effort to exclude individuals with severe pediatric diseases. -

Hypertrophic cardiomyopathy 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Mar 12, 2019

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. 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. This variant has not been reported in the literature in individuals with MYLK2-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 10 of the MYLK2 gene. It does not directly change the encoded amino acid sequence of the MYLK2 protein. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	10
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00041
dbscSNV1_RF	Benign	0.22
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: rs200234935; hg19: chr20-30419500;