chrX-150718858-C-T

Position:

• chrX-150718858-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000445323.7(MTMR1):​c.352+158C>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 0.56 (13000 hom., 17202 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: MTMR1 ENST00000445323.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.798

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant X-150718858-C-T is Benign according to our data. Variant chrX-150718858-C-T is described in ClinVar as [Benign]. Clinvar id is 1181836.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTMR1	NM_001306144.3	c.352+158C>T		intron_variant		ENST00000445323.7	NP_001293073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTMR1	ENST00000445323.7	c.352+158C>T		intron_variant		1	NM_001306144.3	ENSP00000414178	A2

Frequencies

GnomAD3 genomes AF: 0.563 AC: 60982 AN: 108397 Hom.: 13002 Cov.: 20 AF XY: 0.559 AC XY: 17182 AN XY: 30731

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.470

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.534

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.562 AC: 60990 AN: 108443 Hom.: 13000 Cov.: 20 AF XY: 0.559 AC XY: 17202 AN XY: 30789

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.536

Alfa AF: 0.621 Hom.: 19042

Bravo AF: 0.540

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs528861; hg19: chrX-149887330;