X-150718858-C-T

Variant names:

• chrX-150718858-C-T
• rs528861
• NM_001306144.3:c.352+158C>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001306144.3(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 NM_001306144.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.798
• Publications: 2 publications found

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

Our verdict: Likely_benign. The variant received -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 VariationId is 1181836.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001306144.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTMR1	NM_001306144.3	MANE Select	c.352+158C>T		intron	N/A	NP_001293073.1	F8WA39
	MTMR1	NM_001353990.2		c.379+158C>T		intron	N/A	NP_001340919.1	E9PPP8
	MTMR1	NM_003828.5		c.328+158C>T		intron	N/A	NP_003819.1	Q13613-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTMR1	ENST00000445323.7	TSL:1 MANE Select	c.352+158C>T		intron	N/A	ENSP00000414178.2	F8WA39
	MTMR1	ENST00000370390.7	TSL:1	c.328+158C>T		intron	N/A	ENSP00000359417.3	Q13613-1
	MTMR1	ENST00000542156.5	TSL:1	c.328+158C>T		intron	N/A	ENSP00000445281.1	Q8NEC6

Frequencies

GnomAD3 genomes AF: 0.563 AC: 60982 AN: 108397 Hom.: 13002 Cov.: 20

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

African (AFR) AF: 0.388 AC: 11602 AN: 29866

American (AMR) AF: 0.455 AC: 4580 AN: 10063

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 1502 AN: 2595

East Asian (EAS) AF: 0.710 AC: 2432 AN: 3424

South Asian (SAS) AF: 0.389 AC: 971 AN: 2498

European-Finnish (FIN) AF: 0.718 AC: 3888 AN: 5412

Middle Eastern (MID) AF: 0.486 AC: 103 AN: 212

European-Non Finnish (NFE) AF: 0.665 AC: 34732 AN: 52248

Other (OTH) AF: 0.536 AC: 782 AN: 1460

Alfa AF: 0.609 Hom.: 26416

Bravo AF: 0.540

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.74
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs528861; hg19: chrX-149887330;