rs142567411

Positions:

• chr12-110914159-GACAC-G
• chr12-110914159-GACAC-GAC
• chr12-110914159-GACAC-GACACAC
• chr12-110914159-GACAC-GACACACAC
• chr12-110914159-GACAC-GACACACACAC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_000432.4(MYL2):​c.274+23_274+26delGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000085 in 1,223,398 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.000085 (0 hom.)
• Consequence: MYL2 NM_000432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360

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]

MYL2 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 104 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYL2	NM_000432.4	c.274+23_274+26delGTGT		intron_variant		ENST00000228841.15	NP_000423.2
MYL2	NM_001406745.1	c.232+23_232+26delGTGT		intron_variant			NP_001393674.1
MYL2	NM_001406916.1	c.217+23_217+26delGTGT		intron_variant			NP_001393845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000228841.15	c.274+23_274+26delGTGT		intron_variant		1	NM_000432.4	ENSP00000228841.8
MYL2	ENST00000548438.1	c.232+23_232+26delGTGT		intron_variant		3		ENSP00000447154.1
MYL2	ENST00000663220.1	c.217+23_217+26delGTGT		intron_variant				ENSP00000499568.1
MYL2	ENST00000549029.1	n.105+23_105+26delGTGT		intron_variant		2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.0000850 AC: 104 AN: 1223398 Hom.: 0 AF XY: 0.0000682 AC XY: 42 AN XY: 615828

Gnomad4 AFR exome AF: 0.000105

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000128

Gnomad4 FIN exome AF: 0.0000202

Gnomad4 NFE exome AF: 0.000103

Gnomad4 OTH exome AF: 0.0000969

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs142567411; hg19: chr12-111351963;