X-150731781-A-G

Position:

• chrX-150731781-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001306144.3(MTMR1):​c.891+162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 111,270 control chromosomes in the GnomAD database, including 5,552 homozygotes. There are 11,823 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.35 (5552 hom., 11823 hem., cov: 23)
• Consequence: MTMR1 NM_001306144.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.639

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant X-150731781-A-G is Benign according to our data. Variant chrX-150731781-A-G is described in ClinVar as [Benign]. Clinvar id is 1232751.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTMR1	NM_001306144.3	c.891+162A>G		intron_variant		ENST00000445323.7	NP_001293073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTMR1	ENST00000445323.7	c.891+162A>G		intron_variant		1	NM_001306144.3	ENSP00000414178.2

Frequencies

GnomAD3 genomes AF: 0.355 AC: 39453 AN: 111216 Hom.: 5555 Cov.: 23 AF XY: 0.354 AC XY: 11823 AN XY: 33436

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.502

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.354 AC: 39438 AN: 111270 Hom.: 5552 Cov.: 23 AF XY: 0.353 AC XY: 11823 AN XY: 33500

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.372

Alfa AF: 0.426 Hom.: 9830

Bravo AF: 0.346

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.31
DANN	Benign	0.63

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: rs5925417; hg19: chrX-149900253;