chr16-15823340-G-A

Position:

chr16-15823340-G-A

Variant summary

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

The ENST00000300036.6(MYH11):c.417C>T(p.Val139=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,614,076 control chromosomes in the GnomAD database, including 9,794 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 865 hom., cov: 33)

Exomes 𝑓: 0.11 ( 8929 hom. )

Consequence

MYH11
ENST00000300036.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -0.874

Variant links:

Genes affected

MYH11 (HGNC:7569): (myosin heavy chain 11) The protein encoded by this gene is a smooth muscle myosin belonging to the myosin heavy chain family. The gene product is a subunit of a hexameric protein that consists of two heavy chain subunits and two pairs of non-identical light chain subunits. It functions as a major contractile protein, converting chemical energy into mechanical energy through the hydrolysis of ATP. A chromosomal rearrangement involving this gene is associated with acute myeloid leukemia of the M4Eo subtype. Mutations in this gene are associated with visceral myopathy, megacystis-microcolon-intestinal hypoperistalsis syndrome 2, and familial thoracic aortic aneurysm 4. [provided by RefSeq, May 2022]

MYH11 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=-0.67).

BP6

Variant 16-15823340-G-A is Benign according to our data. Variant chr16-15823340-G-A is described in ClinVar as [Benign]. Clinvar id is 138366.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-15823340-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.874 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MYH11	NM_002474.3 linkuse as main transcript	c.417C>T	p.Val139=	synonymous_variant	3/41	ENST00000300036.6	NP_002465.1
MYH11	NM_001040113.2 linkuse as main transcript	c.417C>T	p.Val139=	synonymous_variant	3/43	ENST00000452625.7	NP_001035202.1
MYH11	NM_001040114.2 linkuse as main transcript	c.417C>T	p.Val139=	synonymous_variant	3/42		NP_001035203.1
MYH11	NM_022844.3 linkuse as main transcript	c.417C>T	p.Val139=	synonymous_variant	3/42		NP_074035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYH11	ENST00000300036.6 linkuse as main transcript	c.417C>T	p.Val139=	synonymous_variant	3/41	1	NM_002474.3	ENSP00000300036	P3	P35749-1
MYH11	ENST00000452625.7 linkuse as main transcript	c.417C>T	p.Val139=	synonymous_variant	3/43	1	NM_001040113.2	ENSP00000407821		P35749-3

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15662

AN:

152090

Hom.:

864

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0848

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.0945

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0830

Gnomad SAS

AF:

0.0546

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.0994

AC:

24992

AN:

251486

Hom.:

1347

AF XY:

0.0993

AC XY:

13500

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.0869

Gnomad AMR exome

AF:

0.0691

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.0946

Gnomad SAS exome

AF:

0.0599

Gnomad FIN exome

AF:

0.105

Gnomad NFE exome

AF:

0.116

Gnomad OTH exome

AF:

0.105

GnomAD4 exome

AF:

0.108

AC:

157475

AN:

1461868

Hom.:

8929

Cov.:

AF XY:

0.107

AC XY:

77872

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0846

Gnomad4 AMR exome

AF:

0.0690

Gnomad4 ASJ exome

AF:

0.145

Gnomad4 EAS exome

AF:

0.0651

Gnomad4 SAS exome

AF:

0.0625

Gnomad4 FIN exome

AF:

0.105

Gnomad4 NFE exome

AF:

0.114

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.103

AC:

15675

AN:

152208

Hom.:

865

Cov.:

AF XY:

0.102

AC XY:

7594

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.0848

Gnomad4 AMR

AF:

0.0944

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.0834

Gnomad4 SAS

AF:

0.0549

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.118

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.113

Hom.:

592

Bravo

AF:

0.101

Asia WGS

AF:

0.0590

AC:

205

AN:

3478

EpiCase

AF:

0.121

EpiControl

AF:

0.121

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Familial thoracic aortic aneurysm and aortic dissection

Benign:4

Benign, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Oct 02, 2024	- -
Benign, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Apr 08, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Feb 23, 2015	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. -
Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 16, 2018	- -

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 02, 2012	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. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 04, 2013	Val139Val in exon 3 of MYH11: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 11.8% (1012/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs1050111). -

Aortic aneurysm, familial thoracic 4

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 30, 2023	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

7.2

DANN

Benign

0.86

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