NM_015458.4:c.182+1735T>C

Variant names:

• chr8-11286805-T-C
• rs10091637
• NM_015458.4:c.182+1735T>C

Variant summary

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

The NM_015458.4(MTMR9):​c.182+1735T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,870 control chromosomes in the GnomAD database, including 33,933 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 0.66 (33933 hom., cov: 30)
• Consequence: MTMR9 NM_015458.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 6 publications found

Genes affected

MTMR9 (HGNC:14596): (myotubularin related protein 9) This gene encodes a myotubularin-related protein that is atypical to most other members of the myotubularin-related protein family because it has no dual-specificity phosphatase domain. The encoded protein contains a double-helical motif similar to the SET interaction domain, which is thought to have a role in the control of cell proliferation. In mouse, a protein similar to the encoded protein binds with MTMR7, and together they dephosphorylate phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.866 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015458.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTMR9	NM_015458.4	MANE Select	c.182+1735T>C		intron	N/A	NP_056273.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTMR9	ENST00000221086.8	TSL:1 MANE Select	c.182+1735T>C		intron	N/A	ENSP00000221086.3
	MTMR9	ENST00000530200.1	TSL:1	n.182+1735T>C		intron	N/A	ENSP00000436046.1
	MTMR9	ENST00000526292.1	TSL:2	c.-74+1489T>C		intron	N/A	ENSP00000433239.1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99454 AN: 151752 Hom.: 33888 Cov.: 30

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.656 AC: 99554 AN: 151870 Hom.: 33933 Cov.: 30 AF XY: 0.655 AC XY: 48624 AN XY: 74226

African (AFR) AF: 0.837 AC: 34653 AN: 41400

American (AMR) AF: 0.585 AC: 8930 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4586 AN: 5170

South Asian (SAS) AF: 0.678 AC: 3268 AN: 4818

European-Finnish (FIN) AF: 0.561 AC: 5896 AN: 10504

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38208 AN: 67940

Other (OTH) AF: 0.645 AC: 1362 AN: 2110

Alfa AF: 0.609 Hom.: 4097

Bravo AF: 0.667

Asia WGS AF: 0.789 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.54
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10091637; hg19: chr8-11144314;