dbSNP rs382872: MYH6:p.Asp1660Asp (chr14-23386111-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002471.4(MYH6):c.4980C>T(p.Asp1660Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 1,614,156 control chromosomes in the GnomAD database, including 9,226 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.076 ( 539 hom., cov: 31)

Exomes 𝑓: 0.10 ( 8687 hom. )

Consequence

MYH6
NM_002471.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -0.151

Variant links:

Genes affected

MYH6 (HGNC:7576): (myosin heavy chain 6) Cardiac muscle myosin is a hexamer consisting of two heavy chain subunits, two light chain subunits, and two regulatory subunits. This gene encodes the alpha heavy chain subunit of cardiac myosin. The gene is located approximately 4kb downstream of the gene encoding the beta heavy chain subunit of cardiac myosin. Mutations in this gene cause familial hypertrophic cardiomyopathy and atrial septal defect 3. [provided by RefSeq, Feb 2017]

MYH6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 14-23386111-G-A is Benign according to our data. Variant chr14-23386111-G-A is described in ClinVar as [Benign]. Clinvar id is 44528.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-23386111-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.151 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH6	NM_002471.4 link	c.4980C>T	p.Asp1660Asp	synonymous_variant	Exon 34 of 39	ENST00000405093.9	NP_002462.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH6	ENST00000405093.9 link	c.4980C>T	p.Asp1660Asp	synonymous_variant	Exon 34 of 39	5	NM_002471.4	ENSP00000386041.3		P13533

Frequencies

GnomAD3 genomes

AF:

0.0761

AC:

11578

AN:

152152

Hom.:

538

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0310

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.0546

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0317

Gnomad FIN

AF:

0.0902

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.0721

GnomAD3 exomes

AF:

0.0754

AC:

18958

AN:

251326

Hom.:

921

AF XY:

0.0759

AC XY:

10312

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.0300

Gnomad AMR exome

AF:

0.0356

Gnomad ASJ exome

AF:

0.130

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0386

Gnomad FIN exome

AF:

0.0859

Gnomad NFE exome

AF:

0.108

Gnomad OTH exome

AF:

0.0901

GnomAD4 exome

AF:

0.103

AC:

149850

AN:

1461886

Hom.:

8687

Cov.:

AF XY:

0.101

AC XY:

73280

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0271

Gnomad4 AMR exome

AF:

0.0374

Gnomad4 ASJ exome

AF:

0.130

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.0395

Gnomad4 FIN exome

AF:

0.0841

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.0969

GnomAD4 genome

AF:

0.0761

AC:

11581

AN:

152270

Hom.:

539

Cov.:

AF XY:

0.0746

AC XY:

5553

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0310

Gnomad4 AMR

AF:

0.0546

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0317

Gnomad4 FIN

AF:

0.0902

Gnomad4 NFE

AF:

0.113

Gnomad4 OTH

AF:

0.0714

Alfa

AF:

0.101

Hom.:

376

Bravo

AF:

0.0727

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.108

EpiControl

AF:

0.109

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 27, 2011

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Hypertrophic cardiomyopathy 14

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype

Benign:1

Jun 15, 2015

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.10

DANN

Benign

0.88

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

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