Variant chr22-30027471-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000401950.7(MTMR3):c.*1670C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,638 control chromosomes in the GnomAD database, including 12,551 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 12502 hom., cov: 32)

Exomes 𝑓: 0.40 ( 49 hom. )

Consequence

MTMR3
ENST00000401950.7 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.431

Variant links:

Genes affected

MTMR3 (HGNC:7451): (myotubularin related protein 3) This gene encodes a member of the myotubularin dual specificity protein phosphatase gene family. The encoded protein is structurally similar to myotubularin but in addition contains a FYVE domain and an N-terminal PH-GRAM domain. The protein can self-associate and also form heteromers with another myotubularin related protein. The protein binds to phosphoinositide lipids through the PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The encoded protein has been observed to have a perinuclear, possibly membrane-bound, distribution in cells, but it has also been found free in the cytoplasm. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MTMR3 links:

(HGNC:):

links:

HORMAD2-AS1 (HGNC:50729): (HORMAD2 and MTMR3 antisense RNA 1)

HORMAD2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 22-30027471-C-T is Benign according to our data. Variant chr22-30027471-C-T is described in ClinVar as [Benign]. Clinvar id is 1225402.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
MTMR3	NM_021090.4 linkuse as main transcript	c.*1670C>T	3_prime_UTR_variant	20/20	ENST00000401950.7	NP_066576.1
HORMAD2-AS1	NR_110541.2 linkuse as main transcript	n.362-8742G>A	intron_variant, non_coding_transcript_variant
MTMR3	NM_153050.3 linkuse as main transcript	c.*1670C>T	3_prime_UTR_variant	20/20		NP_694690.1
MTMR3	NM_153051.3 linkuse as main transcript	c.*1670C>T	3_prime_UTR_variant	19/19		NP_694691.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTMR3	ENST00000401950.7 linkuse as main transcript	c.*1670C>T	3_prime_UTR_variant	20/20	1	NM_021090.4	ENSP00000384651	P4	Q13615-1
	ENST00000624945.1 linkuse as main transcript	n.766G>A	non_coding_transcript_exon_variant	1/1
HORMAD2-AS1	ENST00000429350.5 linkuse as main transcript	n.335-8742G>A	intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.401

AC:

60933

AN:

151936

Hom.:

12489

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.464

Gnomad ASJ

AF:

0.392

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.366

Gnomad OTH

AF:

0.405

GnomAD4 exome

AF:

0.396

AC:

231

AN:

584

Hom.:

Cov.:

AF XY:

0.368

AC XY:

126

AN XY:

342

show subpopulations

Gnomad4 EAS exome

AF:

0.420

Gnomad4 FIN exome

AF:

0.388

Gnomad4 NFE exome

AF:

0.417

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.401

AC:

60997

AN:

152054

Hom.:

12502

Cov.:

AF XY:

0.406

AC XY:

30164

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.450

Gnomad4 AMR

AF:

0.463

Gnomad4 ASJ

AF:

0.392

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.453

Gnomad4 FIN

AF:

0.424

Gnomad4 NFE

AF:

0.366

Gnomad4 OTH

AF:

0.402

Alfa

AF:

0.373

Hom.:

24306

Bravo

AF:

0.401

Asia WGS

AF:

0.320

AC:

1112

AN:

3478

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	Aug 23, 2019	This variant is associated with the following publications: (PMID: 22971574) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.42

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