Genetic Variant MROH2B:c.2241+8_2241+9insAATAAGATA (chr5-41033829-C-CTATCTTATT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_173489.5(MROH2B):c.2241+8_2241+9insAATAAGATA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 1,324,924 control chromosomes in the GnomAD database, including 54 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., cov: 0)

Exomes 𝑓: 0.0025 ( 52 hom. )

Consequence

MROH2B
NM_173489.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.238

Publications

3 publications found

Variant links:

Genes affected

MROH2B (HGNC:26857): (maestro heat like repeat family member 2B) Predicted to be involved in protein kinase A signaling. Predicted to be located in acrosomal vesicle and sperm midpiece. [provided by Alliance of Genome Resources, Apr 2022]

MROH2B links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173489.5. 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
	MROH2B	NM_173489.5	MANE Select	c.2241+8_2241+9insAATAAGATA		splice_region intron	N/A	NP_775760.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MROH2B	ENST00000399564.5	TSL:1 MANE Select	c.2241+8_2241+9insAATAAGATA	splice_region intron	N/A	ENSP00000382476.4	Q7Z745-1
MROH2B	ENST00000506092.6	TSL:2	c.906+8_906+9insAATAAGATA	splice_region intron	N/A	ENSP00000441504.1	F5GZ06
MROH2B	ENST00000503890.5	TSL:2	n.1203+8_1203+9insAATAAGATA	splice_region intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00379

AC:

553

AN:

146062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000876

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0116

Gnomad ASJ

AF:

0.00330

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00459

Gnomad FIN

AF:

0.00109

Gnomad MID

AF:

0.00329

Gnomad NFE

AF:

0.00434

Gnomad OTH

AF:

0.00855

GnomAD2 exomes

AF:

0.00330

AC:

437

AN:

132376

AF XY:

0.00321

show subpopulations

Gnomad AFR exome

AF:

0.000777

Gnomad AMR exome

AF:

0.00891

Gnomad ASJ exome

AF:

0.00155

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00108

Gnomad NFE exome

AF:

0.00281

Gnomad OTH exome

AF:

0.00329

GnomAD4 exome

AF:

0.00249

AC:

2940

AN:

1178748

Hom.:

Cov.:

AF XY:

0.00272

AC XY:

1597

AN XY:

586840

show subpopulations

African (AFR)

AF:

0.000579

AC:

AN:

27638

American (AMR)

AF:

0.0101

AC:

332

AN:

32784

Ashkenazi Jewish (ASJ)

AF:

0.00234

AC:

AN:

22204

East Asian (EAS)

AF:

0.00

AC:

AN:

34806

South Asian (SAS)

AF:

0.00546

AC:

386

AN:

70742

European-Finnish (FIN)

AF:

0.00205

AC:

AN:

47380

Middle Eastern (MID)

AF:

0.00840

AC:

AN:

5122

European-Non Finnish (NFE)

AF:

0.00210

AC:

1861

AN:

887684

Other (OTH)

AF:

0.00304

AC:

153

AN:

50388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

111

222

332

443

554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.00380

AC:

555

AN:

146176

Hom.:

Cov.:

AF XY:

0.00410

AC XY:

292

AN XY:

71304

show subpopulations

African (AFR)

AF:

0.000873

AC:

AN:

38950

American (AMR)

AF:

0.0117

AC:

172

AN:

14678

Ashkenazi Jewish (ASJ)

AF:

0.00330

AC:

AN:

3336

East Asian (EAS)

AF:

0.00

AC:

AN:

5046

South Asian (SAS)

AF:

0.00459

AC:

AN:

4576

European-Finnish (FIN)

AF:

0.00109

AC:

AN:

10074

Middle Eastern (MID)

AF:

0.00355

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.00434

AC:

288

AN:

66350

Other (OTH)

AF:

0.00847

AC:

AN:

2008

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

121

151

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:

0.00103

Hom.:

640

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.24

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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