8-17355620-T-C

Position:

• chr8-17355620-T-C

Variant summary

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

The NM_004686.5(MTMR7):​c.468+5497A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,596 control chromosomes in the GnomAD database, including 7,543 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 0.29 (7543 hom., cov: 32)
• Consequence: MTMR7 NM_004686.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTMR7	NM_004686.5	c.468+5497A>G		intron_variant		ENST00000180173.10	NP_004677.3
LOC102724838	XR_428318.4	n.201+10375T>C		intron_variant, non_coding_transcript_variant
MTMR7	XM_047422407.1	c.120+5497A>G		intron_variant			XP_047278363.1
MTMR7	XM_047422408.1	c.468+5497A>G		intron_variant			XP_047278364.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTMR7	ENST00000180173.10	c.468+5497A>G		intron_variant		1	NM_004686.5	ENSP00000180173	P1
MTMR7	ENST00000521857.5	c.468+5497A>G		intron_variant		5		ENSP00000429733
MTMR7	ENST00000517317.5	c.311-6539A>G		intron_variant, NMD_transcript_variant		5		ENSP00000431000

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44185 AN: 151482 Hom.: 7513 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.292 AC: 44265 AN: 151596 Hom.: 7543 Cov.: 32 AF XY: 0.299 AC XY: 22125 AN XY: 74088

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.275

Alfa AF: 0.209 Hom.: 1863

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.66

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: rs9325808; hg19: chr8-17213129;