ENST00000713800.1:c.-52-41386C>T

Variant names:

• chr12-110961967-G-A
• rs7961663
• ENST00000713800.1:c.-52-41386C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000713800.1(MYL2):​c.-52-41386C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,012 control chromosomes in the GnomAD database, including 27,105 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27105 hom., cov: 32)
• Consequence: MYL2 ENST00000713800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 7 publications found

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]

LINC01405 (HGNC:50688): (long intergenic non-protein coding RNA 1405)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000713800.1	c.-52-41386C>T		intron_variant	Intron 1 of 7			ENSP00000519106.1
MYL2	ENST00000713803.1	c.-146-41292C>T		intron_variant	Intron 1 of 7			ENSP00000519109.1
MYL2	ENST00000713805.1	c.-56-41382C>T		intron_variant	Intron 1 of 7			ENSP00000519111.1

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89640 AN: 151894 Hom.: 27071 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.567

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.590 AC: 89723 AN: 152012 Hom.: 27105 Cov.: 32 AF XY: 0.591 AC XY: 43899 AN XY: 74292

African (AFR) AF: 0.691 AC: 28639 AN: 41462

American (AMR) AF: 0.621 AC: 9489 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2241 AN: 5166

South Asian (SAS) AF: 0.661 AC: 3192 AN: 4828

European-Finnish (FIN) AF: 0.553 AC: 5829 AN: 10534

Middle Eastern (MID) AF: 0.610 AC: 177 AN: 290

European-Non Finnish (NFE) AF: 0.547 AC: 37210 AN: 67964

Other (OTH) AF: 0.565 AC: 1193 AN: 2112

Alfa AF: 0.555 Hom.: 35510

Bravo AF: 0.596

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.65
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7961663; hg19: chr12-111399771;