dbSNP rs2361502: MROH2A:c.571+130T>C (chr2-233790144-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001394639.1(MROH2A):c.571+130T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 918,056 control chromosomes in the GnomAD database, including 40,448 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 6943 hom., cov: 31)

Exomes 𝑓: 0.29 ( 33505 hom. )

Consequence

MROH2A
NM_001394639.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.657

Publications

21 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MROH2A	NM_001394639.1 link	c.571+130T>C		intron_variant	Intron 5 of 41	ENST00000389758.4	NP_001381568.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MROH2A	ENST00000389758.4 link	c.571+130T>C	intron_variant	Intron 5 of 41	5	NM_001394639.1	ENSP00000374408.3	A6NES4
MROH2A	ENST00000610772.4 link	c.571+130T>C	intron_variant	Intron 5 of 41	5		ENSP00000477597.1	A0A087WT58
MROH2A	ENST00000480634.2 link	n.183-3529T>C	intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45449

AN:

151816

Hom.:

6940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.361

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.290

Gnomad OTH

AF:

0.276

GnomAD4 exome

AF:

0.291

AC:

222991

AN:

766122

Hom.:

33505

AF XY:

0.293

AC XY:

112162

AN XY:

382606

show subpopulations

African (AFR)

AF:

0.339

AC:

6277

AN:

18518

American (AMR)

AF:

0.287

AC:

5208

AN:

18170

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

4809

AN:

14976

East Asian (EAS)

AF:

0.108

AC:

3414

AN:

31482

South Asian (SAS)

AF:

0.372

AC:

16139

AN:

43384

European-Finnish (FIN)

AF:

0.301

AC:

9267

AN:

30748

Middle Eastern (MID)

AF:

0.304

AC:

795

AN:

2612

European-Non Finnish (NFE)

AF:

0.292

AC:

166685

AN:

570160

Other (OTH)

AF:

0.288

AC:

10397

AN:

36072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

7677

15354

23032

30709

38386

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4670

9340

14010

18680

23350

<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:

0.299

AC:

45478

AN:

151934

Hom.:

6943

Cov.:

AF XY:

0.301

AC XY:

22380

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.330

AC:

13661

AN:

41418

American (AMR)

AF:

0.286

AC:

4366

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1091

AN:

3466

East Asian (EAS)

AF:

0.130

AC:

671

AN:

5170

South Asian (SAS)

AF:

0.361

AC:

1734

AN:

4806

European-Finnish (FIN)

AF:

0.310

AC:

3276

AN:

10564

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.290

AC:

19694

AN:

67928

Other (OTH)

AF:

0.273

AC:

575

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1623

3247

4870

6494

8117

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.294

Hom.:

28229

Bravo

AF:

0.298

Asia WGS

AF:

0.232

AC:

805

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.43

(source)

DANN

Benign

0.64

PhyloP100

-0.66

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over