rs2293855

Positions:

• chr8-11319901-G-A

Variant summary

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

The ENST00000221086.8(MTMR9):​c.1486+63G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,552,686 control chromosomes in the GnomAD database, including 131,317 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 (11066 hom., cov: 32)
  • Exomes 𝑓: 0.41 (120251 hom.)
• Consequence: MTMR9 ENST00000221086.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

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]

(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 = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTMR9	NM_015458.4	c.1486+63G>A		intron_variant		ENST00000221086.8	NP_056273.2
MTMR9	XM_011543831.3	c.898+63G>A		intron_variant			XP_011542133.1
MTMR9	XM_047422125.1	c.1486+63G>A		intron_variant			XP_047278081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTMR9	ENST00000221086.8	c.1486+63G>A		intron_variant		1	NM_015458.4	ENSP00000221086	P1
	ENST00000498997.3	n.1814C>T		non_coding_transcript_exon_variant	2/2	1
MTMR9	ENST00000530200.1	c.*1232+63G>A		intron_variant, NMD_transcript_variant		1		ENSP00000436046
MTMR9	ENST00000526292.1	c.1231+63G>A		intron_variant		2		ENSP00000433239

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54633 AN: 151958 Hom.: 11066 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.371

GnomAD4 exome AF: 0.409 AC: 573009 AN: 1400610 Hom.: 120251 Cov.: 21 AF XY: 0.411 AC XY: 286146 AN XY: 695604

Gnomad4 AFR exome AF: 0.171

Gnomad4 AMR exome AF: 0.355

Gnomad4 ASJ exome AF: 0.338

Gnomad4 EAS exome AF: 0.675

Gnomad4 SAS exome AF: 0.475

Gnomad4 FIN exome AF: 0.456

Gnomad4 NFE exome AF: 0.404

Gnomad4 OTH exome AF: 0.398

GnomAD4 genome AF: 0.359 AC: 54645 AN: 152076 Hom.: 11066 Cov.: 32 AF XY: 0.367 AC XY: 27267 AN XY: 74344

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.370

Alfa AF: 0.354 Hom.: 1662

Bravo AF: 0.347

Asia WGS AF: 0.517 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs2293855; hg19: chr8-11177410; COSMIC: COSV55315894;