Variant 17-58495103-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_001378067.1(MTMR4):c.3081A>T(p.Gly1027Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00545 in 1,613,764 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0058 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0054 ( 32 hom. )

Consequence

MTMR4
NM_001378067.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.29

Variant links:

Genes affected

MTMR4 (HGNC:7452): (myotubularin related protein 4) Enables protein phosphatase binding activity. Involved in regulation of phosphatidylinositol dephosphorylation. Located in endosome. [provided by Alliance of Genome Resources, Apr 2022]

MTMR4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 17-58495103-T-A is Benign according to our data. Variant chr17-58495103-T-A is described in ClinVar as [Benign]. Clinvar id is 779457.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.29 with no splicing effect.

BS2

High AC in GnomAd4 at 886 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTMR4	NM_001378067.1 linkuse as main transcript	c.3081A>T	p.Gly1027Gly	synonymous_variant	15/18	ENST00000682306.1	NP_001364996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MTMR4	ENST00000682306.1 linkuse as main transcript	c.3081A>T	p.Gly1027Gly	synonymous_variant	15/18		NM_001378067.1	ENSP00000507664.1	A0A804HJV7
MTMR4	ENST00000323456.9 linkuse as main transcript	c.3039A>T	p.Gly1013Gly	synonymous_variant	16/19	1		ENSP00000325285.5	Q9NYA4
MTMR4	ENST00000579925.5 linkuse as main transcript	c.2868A>T	p.Gly956Gly	synonymous_variant	15/18	5		ENSP00000464067.1	J3QR65

Frequencies

GnomAD3 genomes

AF:

0.00582

AC:

883

AN:

151754

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00935

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00480

Gnomad ASJ

AF:

0.00347

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000379

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00577

Gnomad OTH

AF:

0.00529

GnomAD3 exomes

AF:

0.00422

AC:

1061

AN:

251494

Hom.:

AF XY:

0.00427

AC XY:

581

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.0100

Gnomad AMR exome

AF:

0.00384

Gnomad ASJ exome

AF:

0.00427

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00170

Gnomad FIN exome

AF:

0.000323

Gnomad NFE exome

AF:

0.00551

Gnomad OTH exome

AF:

0.00586

GnomAD4 exome

AF:

0.00541

AC:

7907

AN:

1461892

Hom.:

Cov.:

AF XY:

0.00539

AC XY:

3919

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.00890

Gnomad4 AMR exome

AF:

0.00382

Gnomad4 ASJ exome

AF:

0.00413

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00154

Gnomad4 FIN exome

AF:

0.000524

Gnomad4 NFE exome

AF:

0.00610

Gnomad4 OTH exome

AF:

0.00566

GnomAD4 genome

AF:

0.00583

AC:

886

AN:

151872

Hom.:

Cov.:

AF XY:

0.00596

AC XY:

442

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.00939

Gnomad4 AMR

AF:

0.00479

Gnomad4 ASJ

AF:

0.00347

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.000379

Gnomad4 NFE

AF:

0.00577

Gnomad4 OTH

AF:

0.00523

Alfa

AF:

0.00572

Hom.:

Bravo

AF:

0.00603

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00665

EpiControl

AF:

0.00622

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 15, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.18

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