16-15837962-G-A

Position:

• chr16-15837962-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BS1 BS2

The NM_002474.3(MYH11):​c.291C>T​(p.Asn97Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00159 in 1,614,118 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0013 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0016 (8 hom.)
• Consequence: MYH11 NM_002474.3 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:11
• Conservation: PhyloP100: 0.0300

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 16-15837962-G-A is Benign according to our data. Variant chr16-15837962-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 138364.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-15837962-G-A is described in Lovd as [Likely_benign]. Variant chr16-15837962-G-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=0.03 with no splicing effect.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0013 (198/152226) while in subpopulation SAS AF= 0.00622 (30/4820). AF 95% confidence interval is 0.00448. There are 1 homozygotes in gnomad4. There are 95 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 8 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYH11	NM_002474.3	c.291C>T	p.Asn97Asn	synonymous_variant	2/41	ENST00000300036.6	NP_002465.1
MYH11	NM_001040113.2	c.291C>T	p.Asn97Asn	synonymous_variant	2/43	ENST00000452625.7	NP_001035202.1
MYH11	NM_001040114.2	c.291C>T	p.Asn97Asn	synonymous_variant	2/42		NP_001035203.1
MYH11	NM_022844.3	c.291C>T	p.Asn97Asn	synonymous_variant	2/42		NP_074035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYH11	ENST00000300036.6	c.291C>T	p.Asn97Asn	synonymous_variant	2/41	1	NM_002474.3	ENSP00000300036.5
MYH11	ENST00000452625.7	c.291C>T	p.Asn97Asn	synonymous_variant	2/43	1	NM_001040113.2	ENSP00000407821.2

Frequencies

GnomAD3 genomes AF: 0.00130 AC: 198 AN: 152108 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000579

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00177

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00643

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00144

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.00180 AC: 453 AN: 251474 Hom.: 1 AF XY: 0.00205 AC XY: 278 AN XY: 135914

Gnomad AFR exome AF: 0.000492

Gnomad AMR exome AF: 0.00127

Gnomad ASJ exome AF: 0.00347

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00467

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00182

Gnomad OTH exome AF: 0.00244

GnomAD4 exome AF: 0.00162 AC: 2366 AN: 1461892 Hom.: 8 Cov.: 32 AF XY: 0.00173 AC XY: 1260 AN XY: 727248

Gnomad4 AFR exome AF: 0.000597

Gnomad4 AMR exome AF: 0.00134

Gnomad4 ASJ exome AF: 0.00390

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00489

Gnomad4 FIN exome AF: 0.0000562

Gnomad4 NFE exome AF: 0.00144

Gnomad4 OTH exome AF: 0.00220

GnomAD4 genome AF: 0.00130 AC: 198 AN: 152226 Hom.: 1 Cov.: 31 AF XY: 0.00128 AC XY: 95 AN XY: 74440

Gnomad4 AFR AF: 0.000602

Gnomad4 AMR AF: 0.00177

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00144

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00139 Hom.: 0

Bravo AF: 0.00125

Asia WGS AF: 0.00202 AC: 7 AN: 3478

EpiCase AF: 0.00196

EpiControl AF: 0.00302

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:4

Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 05, 2016	Variant summary: The MYH11 c.291C>T (p.Asn97Asn) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a damaging outcome for this substitution while 5/5 splice prediction tools predict the variant not to impact normal splicing. This variant was found in 235/121412 control chromosomes, predominantly observed in the South Asian subpopulation at a frequency of 0.0050872 (84/16512). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic MYH11 variant (0.0000013), suggesting this is likely a benign polymorphism found primarily in the populations of South Asian origin. The variant of interest has not, to our knowledge, been reported in affected individuals with strong evidence for causality; nor evaluated for functional impact by in vivo/vitro studies. Multiple clinical diagnostic laboratories classified this variant as benign. Considering the high prevalence of the variant in the general population, it was classified as benign. -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2024	MYH11: BP4, BP7 -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 31, 2022	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Familial thoracic aortic aneurysm and aortic dissection Benign:3

Benign, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 05, 2024	- -
Benign, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Jun 23, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 07, 2018	- -

Aortic aneurysm, familial thoracic 4 Benign:2

Likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 29, 2013

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. -

Cardiovascular phenotype Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 04, 2016

This alteration is classified as likely benign based on a combination of the following: 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	-0.57
CADD	Benign	0.16
DANN	Benign	0.61

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: rs113363750; hg19: chr16-15931819; COSMIC: COSV55557655;