Variant X-150718584-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The ENST00000445323.7(MTMR1):c.277-41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.92 ( 3494 hom., 3912 hem., cov: 0)

Exomes 𝑓: 0.78 ( 19137 hom. 49193 hem. )

Failed GnomAD Quality Control

Consequence

MTMR1
ENST00000445323.7 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.00

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant X-150718584-C-T is Benign according to our data. Variant chrX-150718584-C-T is described in ClinVar as [Benign]. Clinvar id is 1231508.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTMR1	NM_001306144.3 linkuse as main transcript	c.277-41C>T		intron_variant		ENST00000445323.7	NP_001293073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTMR1	ENST00000445323.7 linkuse as main transcript	c.277-41C>T		intron_variant		1	NM_001306144.3	ENSP00000414178	A2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

11443

AN:

12502

Hom.:

3493

Cov.:

AF XY:

0.995

AC XY:

3906

AN XY:

3924

FAILED QC

Gnomad AFR

AF:

0.938

Gnomad AMI

AF:

0.845

Gnomad AMR

AF:

0.895

Gnomad ASJ

AF:

0.902

Gnomad EAS

AF:

0.931

Gnomad SAS

AF:

0.970

Gnomad FIN

AF:

0.981

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.898

Gnomad OTH

AF:

0.903

GnomAD3 exomes

AF:

0.929

AC:

62087

AN:

66838

Hom.:

20452

AF XY:

0.978

AC XY:

21155

AN XY:

21636

show subpopulations

Gnomad AFR exome

AF:

0.699

Gnomad AMR exome

AF:

0.891

Gnomad ASJ exome

AF:

0.969

Gnomad EAS exome

AF:

0.929

Gnomad SAS exome

AF:

0.958

Gnomad FIN exome

AF:

0.992

Gnomad NFE exome

AF:

0.963

Gnomad OTH exome

AF:

0.917

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.781

AC:

91708

AN:

117434

Hom.:

19137

Cov.:

AF XY:

0.957

AC XY:

49193

AN XY:

51406

show subpopulations

Gnomad4 AFR exome

AF:

0.822

Gnomad4 AMR exome

AF:

0.964

Gnomad4 ASJ exome

AF:

0.915

Gnomad4 EAS exome

AF:

0.913

Gnomad4 SAS exome

AF:

0.960

Gnomad4 FIN exome

AF:

0.972

Gnomad4 NFE exome

AF:

0.701

Gnomad4 OTH exome

AF:

0.794

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.915

AC:

11450

AN:

12508

Hom.:

3494

Cov.:

AF XY:

0.995

AC XY:

3912

AN XY:

3930

show subpopulations

Gnomad4 AFR

AF:

0.938

Gnomad4 AMR

AF:

0.895

Gnomad4 ASJ

AF:

0.902

Gnomad4 EAS

AF:

0.931

Gnomad4 SAS

AF:

0.970

Gnomad4 FIN

AF:

0.981

Gnomad4 NFE

AF:

0.898

Gnomad4 OTH

AF:

0.908

Alfa

AF:

0.861

Hom.:

8507

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.8

DANN

Benign

0.42

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