Variant X-150698971-CTTTG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001306144.3(MTMR1):c.147-219_147-216delTTTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 936 hom., 4429 hem., cov: 19)

Consequence

MTMR1
NM_001306144.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.506

Variant links:

Genes affected

MTMR1 (HGNC:7449): (myotubularin related protein 1) This gene encodes a member of the myotubularin related family of proteins. Members of this family contain the consensus sequence for the active site of protein tyrosine phosphatases. Alternatively spliced variants have been described but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

MTMR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-150698971-CTTTG-C is Benign according to our data. Variant chrX-150698971-CTTTG-C is described in ClinVar as [Benign]. Clinvar id is 1233021.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTMR1	NM_001306144.3 link	c.147-219_147-216delTTTG		intron_variant		ENST00000445323.7	NP_001293073.1	F8WA39

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTMR1	ENST00000445323.7 link	c.147-223_147-220delTTTG		intron_variant		1	NM_001306144.3	ENSP00000414178.2		F8WA39

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

15727

AN:

111164

Hom.:

933

Cov.:

AF XY:

0.132

AC XY:

4415

AN XY:

33446

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.0364

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.00470

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.160

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.141

AC:

15735

AN:

111216

Hom.:

936

Cov.:

AF XY:

0.132

AC XY:

4429

AN XY:

33510

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.100

Gnomad4 ASJ

AF:

0.223

Gnomad4 EAS

AF:

0.00472

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.159

Alfa

AF:

0.138

Hom.:

760

Bravo

AF:

0.145

Asia WGS

AF:

0.0860

AC:

215

AN:

2521

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over