chr8-11312700-G-A

Variant names:

• chr8-11312700-G-A
• rs11250127
• NM_015458.4:c.972-2223G>A

Variant summary

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

The NM_015458.4(MTMR9):​c.972-2223G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,106 control chromosomes in the GnomAD database, including 11,263 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 0.36 (11263 hom., cov: 33)
• Consequence: MTMR9 NM_015458.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTMR9	NM_015458.4	c.972-2223G>A		intron_variant	Intron 6 of 9	ENST00000221086.8	NP_056273.2
MTMR9	XM_047422125.1	c.972-2223G>A		intron_variant	Intron 6 of 10		XP_047278081.1
MTMR9	XM_011543831.3	c.384-2223G>A		intron_variant	Intron 4 of 7		XP_011542133.1
MTMR9	XM_017013753.3	c.972-2165G>A		intron_variant	Intron 6 of 6		XP_016869242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTMR9	ENST00000221086.8	c.972-2223G>A		intron_variant	Intron 6 of 9	1	NM_015458.4	ENSP00000221086.3
MTMR9	ENST00000530200.1	n.*718-2223G>A		intron_variant	Intron 7 of 10	1		ENSP00000436046.1
MTMR9	ENST00000526292.1	c.717-2223G>A		intron_variant	Intron 6 of 9	2		ENSP00000433239.1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55096 AN: 151988 Hom.: 11262 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.362 AC: 55110 AN: 152106 Hom.: 11263 Cov.: 33 AF XY: 0.370 AC XY: 27510 AN XY: 74344

African (AFR) AF: 0.185 AC: 7674 AN: 41510

American (AMR) AF: 0.394 AC: 6023 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1167 AN: 3466

East Asian (EAS) AF: 0.704 AC: 3646 AN: 5178

South Asian (SAS) AF: 0.479 AC: 2310 AN: 4824

European-Finnish (FIN) AF: 0.485 AC: 5122 AN: 10556

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27774 AN: 67966

Other (OTH) AF: 0.375 AC: 792 AN: 2112

Alfa AF: 0.211 Hom.: 500

Bravo AF: 0.349

Asia WGS AF: 0.521 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.56
PhyloP100		0.25
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: rs11250127; hg19: chr8-11170209;