dbSNP rs2302189: MTMR4:p.Val311Gly (chr17-58506844-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001378067.1(MTMR4):c.932T>G(p.Val311Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 1,611,908 control chromosomes in the GnomAD database, including 122,014 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10265 hom., cov: 32)

Exomes 𝑓: 0.39 ( 111749 hom. )

Consequence

MTMR4
NM_001378067.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.19

Variant links:

Genes affected

MTMR4 (HGNC:7452): (myotubularin related protein 4) Enables protein phosphatase binding activity. Involved in regulation of phosphatidylinositol dephosphorylation. Located in endosome. [provided by Alliance of Genome Resources, Apr 2022]

MTMR4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=5.507469E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTMR4	NM_001378067.1 link	c.932T>G	p.Val311Gly	missense_variant	Exon 9 of 18	ENST00000682306.1	NP_001364996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
MTMR4	ENST00000682306.1 link	c.932T>G	p.Val311Gly	missense_variant	Exon 9 of 18		NM_001378067.1	ENSP00000507664.1	A0A804HJV7
MTMR4	ENST00000323456.9 link	c.890T>G	p.Val297Gly	missense_variant	Exon 10 of 19	1		ENSP00000325285.5	Q9NYA4
MTMR4	ENST00000579925.5 link	c.890T>G	p.Val297Gly	missense_variant	Exon 10 of 18	5		ENSP00000464067.1	J3QR65

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54649

AN:

151762

Hom.:

10253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.275

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.466

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.346

Gnomad MID

AF:

0.331

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.372

GnomAD3 exomes

AF:

0.418

AC:

103741

AN:

248086

Hom.:

22994

AF XY:

0.412

AC XY:

55281

AN XY:

134138

show subpopulations

Gnomad AFR exome

AF:

0.276

Gnomad AMR exome

AF:

0.618

Gnomad ASJ exome

AF:

0.391

Gnomad EAS exome

AF:

0.528

Gnomad SAS exome

AF:

0.421

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.377

Gnomad OTH exome

AF:

0.403

GnomAD4 exome

AF:

0.387

AC:

564844

AN:

1460028

Hom.:

111749

Cov.:

AF XY:

0.386

AC XY:

280422

AN XY:

726242

show subpopulations

Gnomad4 AFR exome

AF:

0.270

Gnomad4 AMR exome

AF:

0.598

Gnomad4 ASJ exome

AF:

0.392

Gnomad4 EAS exome

AF:

0.530

Gnomad4 SAS exome

AF:

0.414

Gnomad4 FIN exome

AF:

0.345

Gnomad4 NFE exome

AF:

0.377

Gnomad4 OTH exome

AF:

0.385

GnomAD4 genome

AF:

0.360

AC:

54678

AN:

151880

Hom.:

10265

Cov.:

AF XY:

0.361

AC XY:

26801

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.275

Gnomad4 AMR

AF:

0.466

Gnomad4 ASJ

AF:

0.388

Gnomad4 EAS

AF:

0.525

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.346

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.369

Alfa

AF:

0.380

Hom.:

26714

Bravo

AF:

0.375

TwinsUK

AF:

0.373

AC:

1382

ALSPAC

AF:

0.391

AC:

1506

ESP6500AA

AF:

0.279

AC:

1228

ESP6500EA

AF:

0.376

AC:

3236

ExAC

AF:

0.410

AC:

49772

Asia WGS

AF:

0.446

AC:

1553

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.090

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.68

D;D

Eigen

Uncertain

0.33

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.47

T;T

MetaRNN

Benign

0.00055

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

.;L

PrimateAI

Benign

0.48

PROVEAN

Uncertain

-2.5

.;D

REVEL

Uncertain

0.55

Sift

Benign

0.28

.;T

Sift4G

Benign

0.35

T;T

Polyphen

0.89

.;P

Vest4

0.14

MPC

1.2

ClinPred

0.037

GERP RS

4.5

Varity_R

0.34

gMVP

0.70

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over