rs566204

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000346299.10(MTMR2):​c.1131C>T​(p.Thr377=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 1,611,344 control chromosomes in the GnomAD database, including 100,716 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 7040 hom., cov: 32)
Exomes 𝑓: 0.35 ( 93676 hom. )

Consequence

MTMR2
ENST00000346299.10 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 0.242
Variant links:
Genes affected
MTMR2 (HGNC:7450): (myotubularin related protein 2) This gene is a member of the myotubularin family of phosphoinositide lipid phosphatases. The encoded protein possesses phosphatase activity towards phosphatidylinositol-3-phosphate and phosphatidylinositol-3,5-bisphosphate. Mutations in this gene are a cause of Charcot-Marie-Tooth disease type 4B, an autosomal recessive demyelinating neuropathy. Alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 11-95847762-G-A is Benign according to our data. Variant chr11-95847762-G-A is described in ClinVar as [Benign]. Clinvar id is 260685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-95847762-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MTMR2NM_016156.6 linkuse as main transcriptc.1131C>T p.Thr377= synonymous_variant 10/15 ENST00000346299.10 NP_057240.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MTMR2ENST00000346299.10 linkuse as main transcriptc.1131C>T p.Thr377= synonymous_variant 10/151 NM_016156.6 ENSP00000345752 P3Q13614-1

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42715
AN:
151768
Hom.:
7036
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.127
Gnomad AMI
AF:
0.352
Gnomad AMR
AF:
0.270
Gnomad ASJ
AF:
0.527
Gnomad EAS
AF:
0.263
Gnomad SAS
AF:
0.156
Gnomad FIN
AF:
0.243
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.379
Gnomad OTH
AF:
0.329
GnomAD3 exomes
AF:
0.298
AC:
74805
AN:
251242
Hom.:
12653
AF XY:
0.300
AC XY:
40719
AN XY:
135786
show subpopulations
Gnomad AFR exome
AF:
0.125
Gnomad AMR exome
AF:
0.204
Gnomad ASJ exome
AF:
0.520
Gnomad EAS exome
AF:
0.266
Gnomad SAS exome
AF:
0.167
Gnomad FIN exome
AF:
0.246
Gnomad NFE exome
AF:
0.379
Gnomad OTH exome
AF:
0.347
GnomAD4 exome
AF:
0.351
AC:
511845
AN:
1459458
Hom.:
93676
Cov.:
38
AF XY:
0.346
AC XY:
251280
AN XY:
726080
show subpopulations
Gnomad4 AFR exome
AF:
0.121
Gnomad4 AMR exome
AF:
0.214
Gnomad4 ASJ exome
AF:
0.519
Gnomad4 EAS exome
AF:
0.294
Gnomad4 SAS exome
AF:
0.169
Gnomad4 FIN exome
AF:
0.248
Gnomad4 NFE exome
AF:
0.381
Gnomad4 OTH exome
AF:
0.345
GnomAD4 genome
AF:
0.281
AC:
42724
AN:
151886
Hom.:
7040
Cov.:
32
AF XY:
0.273
AC XY:
20239
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.127
Gnomad4 AMR
AF:
0.269
Gnomad4 ASJ
AF:
0.527
Gnomad4 EAS
AF:
0.264
Gnomad4 SAS
AF:
0.156
Gnomad4 FIN
AF:
0.243
Gnomad4 NFE
AF:
0.379
Gnomad4 OTH
AF:
0.335
Alfa
AF:
0.365
Hom.:
13296
Bravo
AF:
0.280
Asia WGS
AF:
0.223
AC:
773
AN:
3478
EpiCase
AF:
0.389
EpiControl
AF:
0.386

ClinVar

Significance: Benign
Submissions summary: Benign:10
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Charcot-Marie-Tooth disease type 4B1 Benign:4
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsJun 02, 2017- -
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 05, 2021- -
Benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
not specified Benign:2
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Charcot-Marie-Tooth disease Benign:1
Benign, criteria provided, single submitterclinical testingMolecular Genetics Laboratory, London Health Sciences Centre-- -
Charcot-Marie-Tooth disease type 4 Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
CADD
Benign
5.6
DANN
Benign
0.52

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.

Other links and lift over

dbSNP: rs566204; hg19: chr11-95580926; COSMIC: COSV60578565; COSMIC: COSV60578565; API