18-3067280-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_003803.4(MYOM1):c.5040T>C(p.Gly1680=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 1,602,184 control chromosomes in the GnomAD database, including 198,578 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.56 (25704 hom., cov: 32)
  • Exomes 𝑓: 0.48 (172874 hom.)
• Consequence: MYOM1 NM_003803.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.491

Genes affected

MYOM1 (HGNC:7613): (myomesin 1) The giant protein titin, together with its associated proteins, interconnects the major structure of sarcomeres, the M bands and Z discs. The C-terminal end of the titin string extends into the M line, where it binds tightly to M-band constituents of apparent molecular masses of 190 kD (myomesin 1) and 165 kD (myomesin 2). This protein, myomesin 1, like myomesin 2, titin, and other myofibrillar proteins contains structural modules with strong homology to either fibronectin type III (motif I) or immunoglobulin C2 (motif II) domains. Myomesin 1 and myomesin 2 each have a unique N-terminal region followed by 12 modules of motif I or motif II, in the arrangement II-II-I-I-I-I-I-II-II-II-II-II. The two proteins share 50% sequence identity in this repeat-containing region. The head structure formed by these 2 proteins on one end of the titin string extends into the center of the M band. The integrating structure of the sarcomere arises from muscle-specific members of the superfamily of immunoglobulin-like proteins. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 18-3067280-A-G is Benign according to our data. Variant chr18-3067280-A-G is described in ClinVar as [Benign]. Clinvar id is 226828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.491 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYOM1	NM_003803.4	c.5040T>C	p.Gly1680=	synonymous_variant	38/38	ENST00000356443.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYOM1	ENST00000356443.9	c.5040T>C	p.Gly1680=	synonymous_variant	38/38	1	NM_003803.4	P2
MYOM1	ENST00000261606.11	c.4752T>C	p.Gly1584=	synonymous_variant	37/37	1		A2
MYOM1	ENST00000581804.1	n.530T>C		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85401 AN: 151940 Hom.: 25666 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.501

GnomAD3 exomes AF: 0.498 AC: 116783 AN: 234312 Hom.: 30026 AF XY: 0.500 AC XY: 63562 AN XY: 127104

Gnomad AFR exome AF: 0.788

Gnomad AMR exome AF: 0.348

Gnomad ASJ exome AF: 0.464

Gnomad EAS exome AF: 0.529

Gnomad SAS exome AF: 0.568

Gnomad FIN exome AF: 0.589

Gnomad NFE exome AF: 0.469

Gnomad OTH exome AF: 0.479

GnomAD4 exome AF: 0.484 AC: 701689 AN: 1450126 Hom.: 172874 Cov.: 58 AF XY: 0.485 AC XY: 349646 AN XY: 720332

Gnomad4 AFR exome AF: 0.799

Gnomad4 AMR exome AF: 0.360

Gnomad4 ASJ exome AF: 0.470

Gnomad4 EAS exome AF: 0.540

Gnomad4 SAS exome AF: 0.567

Gnomad4 FIN exome AF: 0.585

Gnomad4 NFE exome AF: 0.465

Gnomad4 OTH exome AF: 0.501

GnomAD4 genome AF: 0.562 AC: 85495 AN: 152058 Hom.: 25704 Cov.: 32 AF XY: 0.564 AC XY: 41922 AN XY: 74316

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.500

Alfa AF: 0.463 Hom.: 24980

Bravo AF: 0.557

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 24, 2014	Gly1680Gly in exon 38 of MYOM1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 46.6% (3990/8554) of European American chromosomes from a broad population by the NHLBI Exome Sequ encing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2230164). -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Feb 07, 2019	This alteration is classified as 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. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 13, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Hypertrophic cardiomyopathy Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.75
Dann	Benign	0.19

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: rs2230164; hg19: chr18-3067278; COSMIC: COSV55294376;