rs2239879

Positions:

• chr8-17338119-T-C
• chr8-17338119-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004686.5(MTMR7):​c.732+3244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,990 control chromosomes in the GnomAD database, including 19,190 homozygotes. 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 0.46 (19190 hom., cov: 32)
• Consequence: MTMR7 NM_004686.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

MTMR7 (HGNC:7454): (myotubularin related protein 7) This gene encodes a member of the myotubularin family of tyrosine/dual-specificity phosphatases. The encoded protein is characterized by four distinct domains that are conserved among all members of the myotubularin family: the glucosyltransferase, Rab-like GTPase activator and myotubularins domain, the Rac-induced recruitment domain, the protein tyrosine phosphatases and dual-specificity phosphatases domain and the suppressor of variegation 3-9, enhancer-of-zeste, and trithorax interaction domain. This protein dephosphorylates the target substrates phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. A pseudogene of this gene is found on chromosome 5. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTMR7	NM_004686.5	c.732+3244A>G		intron_variant		ENST00000180173.10
MTMR7	XM_047422407.1	c.384+3244A>G		intron_variant
MTMR7	XM_047422408.1	c.732+3244A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTMR7	ENST00000180173.10	c.732+3244A>G		intron_variant		1	NM_004686.5	P1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69119 AN: 151872 Hom.: 19134 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.456 AC: 69240 AN: 151990 Hom.: 19190 Cov.: 32 AF XY: 0.457 AC XY: 33941 AN XY: 74278

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.404

Alfa AF: 0.433 Hom.: 2512

Bravo AF: 0.473

Asia WGS AF: 0.552 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.77

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: rs2239879; hg19: chr8-17195628;