8-17348068-T-G

Position:

• chr8-17348068-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.597+885A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,096 control chromosomes in the GnomAD database, including 5,550 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 0.20 (5550 hom., cov: 31)
• Consequence: MTMR7 NM_004686.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

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]

LOC102724838 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTMR7	NM_004686.5	c.597+885A>C		intron_variant		ENST00000180173.10
LOC102724838	XR_428318.4	n.201+2823T>G		intron_variant, non_coding_transcript_variant
MTMR7	XM_047422407.1	c.249+885A>C		intron_variant
MTMR7	XM_047422408.1	c.597+885A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTMR7	ENST00000180173.10	c.597+885A>C		intron_variant		1	NM_004686.5	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30270 AN: 151978 Hom.: 5507 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0437

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.200 AC: 30364 AN: 152096 Hom.: 5550 Cov.: 31 AF XY: 0.209 AC XY: 15546 AN XY: 74340

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.0437

Gnomad4 OTH AF: 0.200

Alfa AF: 0.0843 Hom.: 1758

Bravo AF: 0.217

Asia WGS AF: 0.497 AC: 1726 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.50

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: rs4921542; hg19: chr8-17205577;