rs121913640

Positions:

chr14-23429867-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM1

This summary comes from the ClinGen Evidence Repository: The c.1046T>C (p.Met349Thr) variant in MYH7 has been reported in at least 6 individuals with HCM (PS4_Supporting; Jeschke 1998 PMID:9544842; GeneDx: pers comm., Ambry: pers comm, Invitae: pers comm), 1 of whom also had additional variants in other HCM-associated genes (Ambry pers comm;). Additionally, one of these individuals also had severe, early-onset (<20 yo) presentation of HCM and carried a second de novo MYH7 variant on the second allele that was classified as pathogenic by this expert panel (p.Arg719Trp, ClinVar variation ID:14104). This variant has also been reported in 1 individual with unspecified heart disease, 1 with LVH, and 1 with arrhythmia, and 1 with LVNC with atrial and ventricular septal defect (Ambry pers comm.; GeneDX pers comm.; Invitae pers comm.; OMGL pers comm.). This variant has also been identified in 0.007% (1/15378) of European chromosomes, in gnomAD (v2.1.1; http://gnomad.broadinstitute.org). This represents only a fraction of the total European chromosomes, suggesting low coverage at this locus. Therefore, data from large population studies are insufficient to assess the frequency of this variant and apply PM2. Additionally, since the MYH7 specifications state that PS4 is only applicable if the variant is absent or rare in large population studies, the PS4 criterion was not applied (Kelly 2018 PMID:29300372). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; Walsh 2017 PMID:27532257). Computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In summary, this variant is classified as uncertain significance for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (Kelly 2018 PMID:29300372): PM1. LINK:https://erepo.genome.network/evrepo/ui/classification/CA010092/MONDO:0005045/002

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

MYH7
NM_000257.4 missense

Scores

Clinical Significance

Uncertain significance reviewed by expert panel P:1U:7

Conservation

PhyloP100: 5.88

Variant links:

Genes affected

MYH7 (HGNC:7577): (myosin heavy chain 7) Muscle myosin is a hexameric protein containing 2 heavy chain subunits, 2 alkali light chain subunits, and 2 regulatory light chain subunits. This gene encodes the beta (or slow) heavy chain subunit of cardiac myosin. It is expressed predominantly in normal human ventricle. It is also expressed in skeletal muscle tissues rich in slow-twitch type I muscle fibers. Changes in the relative abundance of this protein and the alpha (or fast) heavy subunit of cardiac myosin correlate with the contractile velocity of cardiac muscle. Its expression is also altered during thyroid hormone depletion and hemodynamic overloading. Mutations in this gene are associated with familial hypertrophic cardiomyopathy, myosin storage myopathy, dilated cardiomyopathy, and Laing distal myopathy. [provided by RefSeq, May 2022]

MYH7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM1

For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYH7	NM_000257.4 linkuse as main transcript	c.1046T>C	p.Met349Thr	missense_variant	12/40	ENST00000355349.4	NP_000248.2
MYH7	NM_001407004.1 linkuse as main transcript	c.1046T>C	p.Met349Thr	missense_variant	11/39		NP_001393933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYH7	ENST00000355349.4 linkuse as main transcript	c.1046T>C	p.Met349Thr	missense_variant	12/40	1	NM_000257.4	ENSP00000347507	P1

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152072

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000479

AC:

AN:

1461842

Hom.:

Cov.:

AF XY:

0.00000550

AC XY:

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000540

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000197

AC:

AN:

152072

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.0000242

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000688

Hom.:

Bravo

AF:

0.0000113

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1Uncertain:7

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Cardiomyopathy

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Aug 28, 2023	This missense variant replaces methionine with threonine at codon 349 of the MYH7 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with hypertrophic cardiomyopathy (PMID: 9544842, 18761664, 24793961, 32894683). In one family, this variant was reported in compound heterozygous state with another de novo pathogenic MYH7 variant in an individual affected with early-onset hypertrophic cardiomyopathy (PMID: 9544842, 18761664). 6 relatives of this individual were asymptomatic heterozygous carriers for this variant. This variant has been identified in 1/31328 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 15, 2023	This missense variant replaces methionine with threonine at codon 349 of the MYH7 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with hypertrophic cardiomyopathy (PMID: 9544842, 18761664, 24793961, 32894683). In one family, this variant was reported in compound heterozygous state with another de novo pathogenic MYH7 variant in an individual affected with early-onset hypertrophic cardiomyopathy (PMID: 9544842, 18761664). 6 relatives of this individual were asymptomatic heterozygous carriers for this variant. This variant has been identified in 1/31328 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Hypertrophic cardiomyopathy

Uncertain:2

Uncertain significance, reviewed by expert panel	curation	ClinGen Cardiomyopathy Variant Curation Expert Panel	Jun 16, 2021	The c.1046T>C (p.Met349Thr) variant in MYH7 has been reported in at least 6 individuals with HCM (PS4_Supporting; Jeschke 1998 PMID:9544842; GeneDx: pers comm., Ambry: pers comm, Invitae: pers comm), 1 of whom also had additional variants in other HCM-associated genes (Ambry pers comm;). Additionally, one of these individuals also had severe, early-onset (<20 yo) presentation of HCM and carried a second de novo MYH7 variant on the second allele that was classified as pathogenic by this expert panel (p.Arg719Trp, ClinVar variation ID:14104). This variant has also been reported in 1 individual with unspecified heart disease, 1 with LVH, and 1 with arrhythmia, and 1 with LVNC with atrial and ventricular septal defect (Ambry pers comm.; GeneDX pers comm.; Invitae pers comm.; OMGL pers comm.). This variant has also been identified in 0.007% (1/15378) of European chromosomes, in gnomAD (v2.1.1; http://gnomad.broadinstitute.org). This represents only a fraction of the total European chromosomes, suggesting low coverage at this locus. Therefore, data from large population studies are insufficient to assess the frequency of this variant and apply PM2. Additionally, since the MYH7 specifications state that PS4 is only applicable if the variant is absent or rare in large population studies, the PS4 criterion was not applied (Kelly 2018 PMID:29300372). This variant lies in the head region of the protein (aa 181-937) and missense variants in this region are statistically more likely to be disease-associated (PM1; Walsh 2017 PMID:27532257). Computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In summary, this variant is classified as uncertain significance for hypertrophic cardiomyopathy in an autosomal dominant manner. MYH7-specific ACMG/AMP criteria applied (Kelly 2018 PMID:29300372): PM1. -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 03, 2024	This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 349 of the MYH7 protein (p.Met349Thr). This variant is present in population databases (rs121913640, gnomAD 0.007%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (HCM) and an early onset form of HCM (PMID: 9544842, 18761664, 32894683). ClinVar contains an entry for this variant (Variation ID: 14094). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MYH7 protein function. This variant is found within a region of MYH7 between codons 181 and 937 that contains the majority of the myosin head domain. Missense variants in this region have been shown to be significantly overrepresented in individuals with hypertrophic cardiomyopathy (PMID: 27532257). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Hypertrophic cardiomyopathy 1

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 1998

- -

Congenital myopathy with fiber type disproportion;C1834481:Dilated cardiomyopathy 1S;C1842160:Myosin storage myopathy;C1850709:Myopathy, myosin storage, autosomal recessive;C3495498:Hypertrophic cardiomyopathy 1;C4552004:MYH7-related skeletal myopathy

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Feb 15, 2022

- -

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Oct 01, 2021

Reported previously in one individual with HCM who also harbored another de novo MYH7 variant on the opposite allele; he M349T variant was maternally inherited and was identified in several other relatives, all of whom were asymptomatic (Jeschke et al., 1998); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID#14094; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 27532257, 9544842, 10900182, 15737656, 18761664, 26272908, 21310275, 11968089) -

Cardiovascular phenotype

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 03, 2019

The c.1046T>C (p.M349T) alteration is located in exon 12 (coding exon 10) of the MYH7 gene. This alteration results from a T to C substitution at nucleotide position 1046, causing the methionine (M) at amino acid position 349 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.34

CardioboostCm

Uncertain

0.20

BayesDel_addAF

Pathogenic

0.24

BayesDel_noAF

Uncertain

0.10

CADD

Uncertain

DANN

Benign

0.88

DEOGEN2

Uncertain

0.67

Eigen

Benign

-0.23

Eigen_PC

Benign

-0.15

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.90

M_CAP

Pathogenic

0.91

MetaRNN

Pathogenic

0.79

MetaSVM

Uncertain

-0.075

MutationAssessor

Benign

0.69

MutationTaster

Benign

0.95

PrimateAI

Benign

0.48

PROVEAN

Benign

-1.2

REVEL

Uncertain

0.58

Sift

Uncertain

0.0070

Sift4G

Uncertain

0.0080

Polyphen

0.0010

Vest4

0.48

MutPred

0.71

Loss of stability (P = 0.0237);

MVP

0.95

MPC

1.2

ClinPred

0.39

GERP RS

3.9

Varity_R

0.50

gMVP

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over