Genetic Variant MROH2A:p.Asn293Asn (chr2-233794419-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001394639.1(MROH2A):c.879C>T(p.Asn293Asn) 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

Publications

3 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394639.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH2A	NM_001394639.1	MANE Select	c.879C>T	p.Asn293Asn	synonymous	Exon 8 of 42	NP_001381568.1	A6NES4
	MROH2A	NM_001367507.1		c.879C>T	p.Asn293Asn	synonymous	Exon 8 of 42	NP_001354436.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH2A	ENST00000389758.4	TSL:5 MANE Select	c.879C>T	p.Asn293Asn	synonymous	Exon 8 of 42	ENSP00000374408.3	A6NES4
	MROH2A	ENST00000610772.4	TSL:5	c.879C>T	p.Asn293Asn	synonymous	Exon 8 of 42	ENSP00000477597.1	A0A087WT58

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

GnomAD2 exomes

AF:

0.00403

AC:

591

AN:

146764

AF XY:

0.00395

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 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

African (AFR)

AF:

0.00133

AC:

AN:

31598

American (AMR)

AF:

0.00527

AC:

188

AN:

35702

Ashkenazi Jewish (ASJ)

AF:

0.00596

AC:

150

AN:

25182

East Asian (EAS)

AF:

0.000224

AC:

AN:

35738

South Asian (SAS)

AF:

0.000606

AC:

AN:

79236

European-Finnish (FIN)

AF:

0.00139

AC:

AN:

48168

Middle Eastern (MID)

AF:

0.000527

AC:

AN:

5698

European-Non Finnish (NFE)

AF:

0.00764

AC:

8238

AN:

1078950

Other (OTH)

AF:

0.00593

AC:

344

AN:

57986

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

453

906

1359

1812

2265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

338

676

1014

1352

1690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00475

AC:

723

AN:

152220

Hom.:

Cov.:

AF XY:

0.00462

AC XY:

344

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.00144

AC:

AN:

41548

American (AMR)

AF:

0.00916

AC:

140

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00576

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5150

South Asian (SAS)

AF:

0.000207

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00123

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00660

AC:

449

AN:

68018

Other (OTH)

AF:

0.00664

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

116

155

194

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00527

Hom.:

Bravo

AF:

0.00566

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.47

(source)

DANN

Benign

0.64

PhyloP100

-0.72

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over