rs2285274

Positions:

• chr8-17310516-G-A

Variant summary

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

The NM_004686.5(MTMR7):​c.1101+995C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,182 control chromosomes in the GnomAD database, including 1,418 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 0.10 (1418 hom., cov: 32)
• Consequence: MTMR7 NM_004686.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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]

VPS37A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTMR7	NM_004686.5	c.1101+995C>T		intron_variant		ENST00000180173.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTMR7	ENST00000180173.10	c.1101+995C>T		intron_variant		1	NM_004686.5	P1
MTMR7	ENST00000521857.5	c.1101+995C>T		intron_variant		5
MTMR7	ENST00000519590.5	n.163+995C>T		intron_variant, non_coding_transcript_variant		4
MTMR7	ENST00000519763.1	n.237+995C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15854 AN: 152064 Hom.: 1409 Cov.: 32

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.104 AC: 15876 AN: 152182 Hom.: 1418 Cov.: 32 AF XY: 0.111 AC XY: 8293 AN XY: 74406

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.0997

Gnomad4 OTH AF: 0.119

Alfa AF: 0.110 Hom.: 1458

Bravo AF: 0.0965

Asia WGS AF: 0.380 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.091
DANN	Benign	0.33

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: rs2285274; hg19: chr8-17168025;