NM_001040113.2:c.5832G>C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The NM_001040113.2(MYH11):c.5832G>C(p.Ser1944Ser) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000249 in 1,608,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S1944S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

MYH11
NM_001040113.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.87

Publications

2 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 links:

NDE1 (HGNC:17619): (nudE neurodevelopment protein 1) This gene encodes a member of the nuclear distribution E (NudE) family of proteins. The encoded protein is localized at the centrosome and interacts with other centrosome components as part of a multiprotein complex that regulates dynein function. This protein plays an essential role in microtubule organization, mitosis and neuronal migration. Mutations in this gene cause lissencephaly 4, a disorder characterized by lissencephaly, severe brain atrophy, microcephaly, and severe cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

NDE1 Gene-Disease associations (from GenCC):

lissencephaly 4
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
hydranencephaly
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
microlissencephaly
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
NDE1-related microhydranencephaly
Inheritance: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

NDE1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (REVEL=0.032).

BP6

Variant 16-15708817-C-G is Benign according to our data. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-15708817-C-G is described in CliVar as Likely_benign. Clinvar id is 2712532.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH11	NM_001040113.2 link	c.5832G>C	p.Ser1944Ser	synonymous_variant	Exon 42 of 43	ENST00000452625.7	NP_001035202.1	P35749-3
MYH11	NM_002474.3 link	c.5787-4694G>C		intron_variant	Intron 40 of 40	ENST00000300036.6	NP_002465.1	P35749-1A0A024QZJ4
NDE1	NM_017668.3 link	c.947+11957C>G		intron_variant	Intron 8 of 8	ENST00000396354.6	NP_060138.1	Q9NXR1-2X5DR54

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
MYH11	ENST00000452625.7 link	c.5832G>C	p.Ser1944Ser	synonymous_variant	Exon 42 of 43	1	NM_001040113.2	ENSP00000407821.2	P35749-3
MYH11	ENST00000300036.6 link	c.5787-4694G>C		intron_variant	Intron 40 of 40	1	NM_002474.3	ENSP00000300036.5	P35749-1
NDE1	ENST00000396354.6 link	c.947+11957C>G		intron_variant	Intron 8 of 8	1	NM_017668.3	ENSP00000379642.1	Q9NXR1-2

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

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:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000414

AC:

AN:

241780

AF XY:

0.00000767

show subpopulations

Gnomad AFR exome

AF:

0.0000663

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000206

AC:

AN:

1456814

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

724006

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33442

American (AMR)

AF:

0.00

AC:

AN:

43876

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25936

East Asian (EAS)

AF:

0.00

AC:

AN:

39650

South Asian (SAS)

AF:

0.00

AC:

AN:

84724

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53096

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.00000180

AC:

AN:

1110100

Other (OTH)

AF:

0.00

AC:

AN:

60228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.00000657

AC:

AN:

152142

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41428

American (AMR)

AF:

0.00

AC:

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5196

South Asian (SAS)

AF:

0.00

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10596

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68040

Other (OTH)

AF:

0.00

AC:

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000113

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Aortic aneurysm, familial thoracic 4

Benign:1

Dec 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

3.9

Mutation Taster

=86/14

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over