chr12-110913150-G-C

Variant names:

• chr12-110913150-G-C
• rs977023771
• NM_000432.4:c.354-6C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 2P and 12B. PM2 BP4_Strong BP6_Very_Strong

The NM_000432.4(MYL2):​c.354-6C>G variant causes a splice region, 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 Likely benign (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MYL2 NM_000432.4 splice_region, intron
• Scores: Splicing: ADA: 0.001211
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.929
• Publications: 0 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]

MYL2 Gene-Disease associations (from GenCC):

• hypertrophic cardiomyopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• hypertrophic cardiomyopathy 10

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• myopathy, myofibrillar, 12, infantile-onset, with cardiomyopathy

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
• congenital fiber-type disproportion myopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• dilated cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 12-110913150-G-C is Benign according to our data. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-110913150-G-C is described in CliVar as Likely_benign. Clinvar id is 1291279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYL2	NM_000432.4	c.354-6C>G		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000228841.15	NP_000423.2
MYL2	NM_001406745.1	c.312-6C>G		splice_region_variant, intron_variant	Intron 4 of 5		NP_001393674.1
MYL2	NM_001406916.1	c.297-6C>G		splice_region_variant, intron_variant	Intron 5 of 6		NP_001393845.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYL2	ENST00000228841.15	c.354-6C>G		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_000432.4	ENSP00000228841.8

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy 10 Benign:1

Jul 28, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Jan 04, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.6
DANN	Benign	0.69
PhyloP100		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0012
dbscSNV1_RF	Benign	0.15
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

Other links and lift over

dbSNP: rs977023771; hg19: chr12-111350954;