chrX-64332496-A-G

Variant names:

• chrX-64332496-A-G
• rs12560201
• NM_017677.4:c.1152-739T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017677.4(MTMR8):​c.1152-739T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 111,763 control chromosomes in the GnomAD database, including 207 homozygotes. There are 1,833 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.060 (207 hom., 1833 hem., cov: 23)
• Consequence: MTMR8 NM_017677.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 1 publications found

Genes affected

MTMR8 (HGNC:16825): (myotubularin related protein 8) This gene encodes a member of the myotubularin-related family and is part of the MTMR6 subgroup. Family members are dual-specificity phosphatases and the encoded protein contains a phosphoinositide-binding domain (PID) and a SET-interacting domain (SID). Defects in other family members have been found in myotubular myopathic diseases. [provided by RefSeq, Mar 2010]

ENSG00000287370 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017677.4. 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
	MTMR8	NM_017677.4	MANE Select	c.1152-739T>C		intron	N/A	NP_060147.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTMR8	ENST00000374852.4	TSL:1 MANE Select	c.1152-739T>C		intron	N/A	ENSP00000363985.3	Q96EF0-1
	MTMR8	ENST00000462447.5	TSL:3	n.312-739T>C		intron	N/A
	MTMR8	ENST00000478487.5	TSL:3	n.351-739T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 6699 AN: 111711 Hom.: 207 Cov.: 23

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0642

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.000845

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0797

Gnomad MID AF: 0.0213

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0599 AC: 6696 AN: 111763 Hom.: 207 Cov.: 23 AF XY: 0.0540 AC XY: 1833 AN XY: 33945

African (AFR) AF: 0.0131 AC: 406 AN: 30882

American (AMR) AF: 0.0354 AC: 374 AN: 10553

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 92 AN: 2634

East Asian (EAS) AF: 0.000848 AC: 3 AN: 3538

South Asian (SAS) AF: 0.0140 AC: 37 AN: 2647

European-Finnish (FIN) AF: 0.0797 AC: 482 AN: 6044

Middle Eastern (MID) AF: 0.0187 AC: 4 AN: 214

European-Non Finnish (NFE) AF: 0.0978 AC: 5187 AN: 53037

Other (OTH) AF: 0.0438 AC: 67 AN: 1529

Alfa AF: 0.0697 Hom.: 1724

Bravo AF: 0.0544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.84
PhyloP100		-0.051
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12560201; hg19: chrX-63552376;