Genetic Variant NM_002474.3:c.2208C>T (chr16-15747916-G-A) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_002474.3(MYH11):c.2208C>T(p.Ile736Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0448 in 1,613,904 control chromosomes in the GnomAD database, including 2,504 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.073 ( 603 hom., cov: 31)

Exomes 𝑓: 0.042 ( 1901 hom. )

Consequence

MYH11
NM_002474.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: 0.387

Publications

9 publications found

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 Gene-Disease associations (from GenCC):

familial thoracic aortic aneurysm and aortic dissection
Inheritance: AD, Unknown Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
aortic aneurysm, familial thoracic 4
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
megacystis-microcolon-intestinal hypoperistalsis syndrome 2
Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
megacystis-microcolon-intestinal hypoperistalsis syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
congenital heart disease
Inheritance: AD Classification: LIMITED Submitted by: ClinGen
visceral myopathy 2
Inheritance: AD, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

MYH11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 16-15747916-G-A is Benign according to our data. Variant chr16-15747916-G-A is described in ClinVar as Benign. ClinVar VariationId is 36616.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.387 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002474.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MYH11	NM_002474.3	MANE Select	c.2208C>T	p.Ile736Ile	synonymous	Exon 18 of 41	NP_002465.1	P35749-1
MYH11	NM_001040113.2	MANE Plus Clinical	c.2229C>T	p.Ile743Ile	synonymous	Exon 19 of 43	NP_001035202.1	P35749-3
MYH11	NM_001040114.2		c.2229C>T	p.Ile743Ile	synonymous	Exon 19 of 42	NP_001035203.1	P35749-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MYH11	ENST00000300036.6	TSL:1 MANE Select	c.2208C>T	p.Ile736Ile	synonymous	Exon 18 of 41	ENSP00000300036.5	P35749-1
MYH11	ENST00000452625.7	TSL:1 MANE Plus Clinical	c.2229C>T	p.Ile743Ile	synonymous	Exon 19 of 43	ENSP00000407821.2	P35749-3
MYH11	ENST00000396324.7	TSL:1	c.2229C>T	p.Ile743Ile	synonymous	Exon 19 of 42	ENSP00000379616.3	P35749-2

Frequencies

GnomAD3 genomes

AF:

0.0727

AC:

11039

AN:

151914

Hom.:

595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.0524

Gnomad ASJ

AF:

0.0265

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.0996

Gnomad FIN

AF:

0.0367

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0355

Gnomad OTH

AF:

0.0662

GnomAD2 exomes

AF:

0.0529

AC:

13315

AN:

251468

AF XY:

0.0538

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.0295

Gnomad ASJ exome

AF:

0.0282

Gnomad EAS exome

AF:

0.109

Gnomad FIN exome

AF:

0.0362

Gnomad NFE exome

AF:

0.0324

Gnomad OTH exome

AF:

0.0430

GnomAD4 exome

AF:

0.0419

AC:

61240

AN:

1461872

Hom.:

1901

Cov.:

AF XY:

0.0431

AC XY:

31314

AN XY:

727238

show subpopulations

African (AFR)

AF:

0.147

AC:

4935

AN:

33480

American (AMR)

AF:

0.0304

AC:

1361

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0264

AC:

691

AN:

26136

East Asian (EAS)

AF:

0.107

AC:

4232

AN:

39700

South Asian (SAS)

AF:

0.0889

AC:

7672

AN:

86258

European-Finnish (FIN)

AF:

0.0365

AC:

1951

AN:

53404

Middle Eastern (MID)

AF:

0.0392

AC:

226

AN:

5768

European-Non Finnish (NFE)

AF:

0.0333

AC:

37082

AN:

1112006

Other (OTH)

AF:

0.0512

AC:

3090

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

4384

8767

13151

17534

21918

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1520

3040

4560

6080

7600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0729

AC:

11076

AN:

152032

Hom.:

603

Cov.:

AF XY:

0.0737

AC XY:

5476

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.147

AC:

6090

AN:

41428

American (AMR)

AF:

0.0523

AC:

798

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0265

AC:

AN:

3470

East Asian (EAS)

AF:

0.107

AC:

552

AN:

5146

South Asian (SAS)

AF:

0.101

AC:

485

AN:

4806

European-Finnish (FIN)

AF:

0.0367

AC:

389

AN:

10604

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0355

AC:

2417

AN:

67994

Other (OTH)

AF:

0.0722

AC:

152

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

501

1002

1504

2005

2506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0472

Hom.:

470

Bravo

AF:

0.0763

Asia WGS

AF:

0.0980

AC:

339

AN:

3478

EpiCase

AF:

0.0348

EpiControl

AF:

0.0342

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

Familial thoracic aortic aneurysm and aortic dissection (3)

Aortic aneurysm, familial thoracic 4 (2)

not provided (2)

Cardiovascular phenotype (1)

Familial aortopathy (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

6.1

(source)

DANN

Benign

0.78

PhyloP100

0.39

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over