dbSNP rs11205303: MTMR11:p.Met159Val (chr1-149934520-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001145862.2(MTMR11):c.475A>G(p.Met159Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 1,613,058 control chromosomes in the GnomAD database, including 116,305 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 7829 hom., cov: 32)

Exomes 𝑓: 0.38 ( 108476 hom. )

Consequence

MTMR11
NM_001145862.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.555

Publications

96 publications found

Variant links:

Genes affected

MTMR11 (HGNC:24307): (myotubularin related protein 11) Predicted to enable phosphatidylinositol-3-phosphatase activity. Predicted to be involved in phosphatidylinositol dephosphorylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MTMR11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0030397177).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTMR11	NM_001145862.2 link	c.475A>G	p.Met159Val	missense_variant	Exon 6 of 17	ENST00000439741.4	NP_001139334.1	A4FU01-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTMR11	ENST00000439741.4 link	c.475A>G	p.Met159Val	missense_variant	Exon 6 of 17	2	NM_001145862.2	ENSP00000391668.2		A4FU01-1

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44016

AN:

152008

Hom.:

7833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0800

Gnomad AMI

AF:

0.499

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.311

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.407

Gnomad OTH

AF:

0.340

GnomAD2 exomes

AF:

0.333

AC:

83545

AN:

251124

AF XY:

0.344

show subpopulations

Gnomad AFR exome

AF:

0.0685

Gnomad AMR exome

AF:

0.240

Gnomad ASJ exome

AF:

0.285

Gnomad EAS exome

AF:

0.332

Gnomad FIN exome

AF:

0.307

Gnomad NFE exome

AF:

0.408

Gnomad OTH exome

AF:

0.354

GnomAD4 exome

AF:

0.379

AC:

553189

AN:

1460928

Hom.:

108476

Cov.:

AF XY:

0.378

AC XY:

275039

AN XY:

726822

show subpopulations

African (AFR)

AF:

0.0649

AC:

2173

AN:

33478

American (AMR)

AF:

0.248

AC:

11082

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

7502

AN:

26128

East Asian (EAS)

AF:

0.263

AC:

10454

AN:

39694

South Asian (SAS)

AF:

0.332

AC:

28625

AN:

86220

European-Finnish (FIN)

AF:

0.316

AC:

16887

AN:

53412

Middle Eastern (MID)

AF:

0.386

AC:

2226

AN:

5768

European-Non Finnish (NFE)

AF:

0.407

AC:

452525

AN:

1111146

Other (OTH)

AF:

0.360

AC:

21715

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

16943

33887

50830

67774

84717

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.289

AC:

44011

AN:

152130

Hom.:

7829

Cov.:

AF XY:

0.284

AC XY:

21089

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.0798

AC:

3316

AN:

41536

American (AMR)

AF:

0.289

AC:

4418

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

995

AN:

3472

East Asian (EAS)

AF:

0.311

AC:

1612

AN:

5176

South Asian (SAS)

AF:

0.312

AC:

1505

AN:

4820

European-Finnish (FIN)

AF:

0.306

AC:

3238

AN:

10568

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.407

AC:

27642

AN:

67966

Other (OTH)

AF:

0.338

AC:

713

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1486

2972

4459

5945

7431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.365

Hom.:

46329

Bravo

AF:

0.283

TwinsUK

AF:

0.400

AC:

1484

ALSPAC

AF:

0.419

AC:

1614

ESP6500AA

AF:

0.0869

AC:

383

ESP6500EA

AF:

0.404

AC:

3473

ExAC

AF:

0.335

AC:

40656

Asia WGS

AF:

0.253

AC:

877

AN:

3478

EpiCase

AF:

0.410

EpiControl

AF:

0.418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

CADD

Benign

(source)

DANN

Benign

0.90

DEOGEN2

Benign

0.016

.;T

Eigen

Benign

-0.47

Eigen_PC

Benign

-0.33

FATHMM_MKL

Benign

0.58

LIST_S2

Benign

0.64

T;T

MetaRNN

Benign

0.0030

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.7

.;L

PhyloP100

0.56

PrimateAI

Benign

0.34

PROVEAN

Benign

-1.1

N;N

REVEL

Benign

0.14

Sift

Benign

0.19

T;T

Sift4G

Benign

0.54

T;T

Polyphen

0.14

B;B

Vest4

0.097

MPC

0.18

ClinPred

0.0086

GERP RS

2.6

Varity_R

0.057

gMVP

0.53

Mutation Taster

=95/5

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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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rs11205303

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over