Variant chr8-11304987-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_015458.4(MTMR9):c.564A>C(p.Leu188=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,613,482 control chromosomes in the GnomAD database, including 139,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 11378 hom., cov: 32)

Exomes 𝑓: 0.41 ( 128116 hom. )

Consequence

MTMR9
NM_015458.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.634

Variant links:

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]

MTMR9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 8-11304987-A-C is Benign according to our data. Variant chr8-11304987-A-C is described in ClinVar as [Benign]. Clinvar id is 1343923.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.634 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MTMR9	NM_015458.4 linkuse as main transcript	c.564A>C	p.Leu188=	synonymous_variant	4/10	ENST00000221086.8
MTMR9	XM_047422125.1 linkuse as main transcript	c.564A>C	p.Leu188=	synonymous_variant	4/11
MTMR9	XM_017013753.3 linkuse as main transcript	c.564A>C	p.Leu188=	synonymous_variant	4/7
MTMR9	XM_011543831.3 linkuse as main transcript	c.-25A>C		5_prime_UTR_variant	2/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTMR9	ENST00000221086.8 linkuse as main transcript	c.564A>C	p.Leu188=	synonymous_variant	4/10	1	NM_015458.4	P1	Q96QG7-1
MTMR9	ENST00000530200.1 linkuse as main transcript	c.*310A>C		3_prime_UTR_variant, NMD_transcript_variant	5/11	1
MTMR9	ENST00000526292.1 linkuse as main transcript	c.309A>C	p.Leu103=	synonymous_variant	4/10	2			Q96QG7-2

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55634

AN:

151912

Hom.:

11377

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.543

Gnomad AMR

AF:

0.397

Gnomad ASJ

AF:

0.337

Gnomad EAS

AF:

0.706

Gnomad SAS

AF:

0.482

Gnomad FIN

AF:

0.485

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.378

GnomAD3 exomes

AF:

0.420

AC:

105254

AN:

250900

Hom.:

23680

AF XY:

0.429

AC XY:

58188

AN XY:

135550

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.347

Gnomad ASJ exome

AF:

0.340

Gnomad EAS exome

AF:

0.733

Gnomad SAS exome

AF:

0.473

Gnomad FIN exome

AF:

0.466

Gnomad NFE exome

AF:

0.409

Gnomad OTH exome

AF:

0.397

GnomAD4 exome

AF:

0.414

AC:

604313

AN:

1461452

Hom.:

128116

Cov.:

AF XY:

0.416

AC XY:

302236

AN XY:

727028

show subpopulations

Gnomad4 AFR exome

AF:

0.187

Gnomad4 AMR exome

AF:

0.354

Gnomad4 ASJ exome

AF:

0.340

Gnomad4 EAS exome

AF:

0.693

Gnomad4 SAS exome

AF:

0.475

Gnomad4 FIN exome

AF:

0.466

Gnomad4 NFE exome

AF:

0.408

Gnomad4 OTH exome

AF:

0.402

GnomAD4 genome

AF:

0.366

AC:

55645

AN:

152030

Hom.:

11378

Cov.:

AF XY:

0.374

AC XY:

27756

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.196

Gnomad4 AMR

AF:

0.397

Gnomad4 ASJ

AF:

0.337

Gnomad4 EAS

AF:

0.706

Gnomad4 SAS

AF:

0.480

Gnomad4 FIN

AF:

0.485

Gnomad4 NFE

AF:

0.409

Gnomad4 OTH

AF:

0.379

Alfa

AF:

0.388

Hom.:

15265

Bravo

AF:

0.354

Asia WGS

AF:

0.522

AC:

1816

AN:

3478

EpiCase

AF:

0.413

EpiControl

AF:

0.413

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 10, 2022	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

5.5

DANN

Benign

0.69

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over