Variant 2-233794419-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001394639.1(MROH2A):c.879C>T(p.Asn293=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00633 in 1,550,478 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 40 hom. )

Consequence

MROH2A
NM_001394639.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.716

Variant links:

Genes affected

MROH2A (HGNC:27936): (maestro heat like repeat family member 2A) This gene encodes a HEAT-domain-containing protein. The function of the encoded protein has not been characterized. [provided by RefSeq, Aug 2016]

MROH2A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 2-233794419-C-T is Benign according to our data. Variant chr2-233794419-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652024.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.716 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MROH2A	NM_001394639.1 linkuse as main transcript	c.879C>T	p.Asn293=	synonymous_variant	8/42	ENST00000389758.4	NP_001381568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MROH2A	ENST00000389758.4 linkuse as main transcript	c.879C>T	p.Asn293=	synonymous_variant	8/42	5	NM_001394639.1	ENSP00000374408	A2
MROH2A	ENST00000610772.4 linkuse as main transcript	c.879C>T	p.Asn293=	synonymous_variant	8/42	5		ENSP00000477597	P4

Frequencies

GnomAD3 genomes

AF:

0.00475

AC:

723

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.00917

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00123

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00660

Gnomad OTH

AF:

0.00671

GnomAD3 exomes

AF:

0.00403

AC:

591

AN:

146764

Hom.:

AF XY:

0.00395

AC XY:

313

AN XY:

79156

show subpopulations

Gnomad AFR exome

AF:

0.00103

Gnomad AMR exome

AF:

0.00497

Gnomad ASJ exome

AF:

0.00681

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000532

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00640

Gnomad OTH exome

AF:

0.00680

GnomAD4 exome

AF:

0.00650

AC:

9088

AN:

1398258

Hom.:

Cov.:

AF XY:

0.00634

AC XY:

4369

AN XY:

689656

show subpopulations

Gnomad4 AFR exome

AF:

0.00133

Gnomad4 AMR exome

AF:

0.00527

Gnomad4 ASJ exome

AF:

0.00596

Gnomad4 EAS exome

AF:

0.000224

Gnomad4 SAS exome

AF:

0.000606

Gnomad4 FIN exome

AF:

0.00139

Gnomad4 NFE exome

AF:

0.00764

Gnomad4 OTH exome

AF:

0.00593

GnomAD4 genome

AF:

0.00475

AC:

723

AN:

152220

Hom.:

Cov.:

AF XY:

0.00462

AC XY:

344

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.00144

Gnomad4 AMR

AF:

0.00916

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00123

Gnomad4 NFE

AF:

0.00660

Gnomad4 OTH

AF:

0.00664

Alfa

AF:

0.00527

Hom.:

Bravo

AF:

0.00566

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

MROH2A: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.47

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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