rs10153321

Variant names:

• chr18-3176379-G-A
• rs10153321
• NM_003803.4:c.930-245C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003803.4(MYOM1):​c.930-245C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,160 control chromosomes in the GnomAD database, including 726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.086 (726 hom., cov: 32)
• Consequence: MYOM1 NM_003803.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

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]

MYOM1 Gene-Disease associations (from GenCC):

• hypertrophic cardiomyopathy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 18-3176379-G-A is Benign according to our data. Variant chr18-3176379-G-A is described in ClinVar as Benign. ClinVar VariationId is 1251258.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYOM1	NM_003803.4	c.930-245C>T		intron_variant	Intron 5 of 37	ENST00000356443.9	NP_003794.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOM1	ENST00000356443.9	c.930-245C>T		intron_variant	Intron 5 of 37	1	NM_003803.4	ENSP00000348821.4
MYOM1	ENST00000261606.11	c.930-245C>T		intron_variant	Intron 5 of 36	1		ENSP00000261606.7

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13156 AN: 152042 Hom.: 724 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0749

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.0725

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.0865 AC: 13161 AN: 152160 Hom.: 726 Cov.: 32 AF XY: 0.0875 AC XY: 6512 AN XY: 74388

African (AFR) AF: 0.150 AC: 6237 AN: 41490

American (AMR) AF: 0.0710 AC: 1085 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0864 AC: 300 AN: 3472

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5180

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4824

European-Finnish (FIN) AF: 0.0725 AC: 767 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0590 AC: 4011 AN: 68022

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0679 Hom.: 664

Bravo AF: 0.0891

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 01, 2019

GeneDx

Significance: 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	-0.94
CADD	Benign	1.6
DANN	Benign	0.39
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10153321; hg19: chr18-3176377;