Genetic Variant MROH2B:c.2241+8_2241+9insAATAGATA (chr5-41033829-C-CTATCTATT) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_173489.5(MROH2B):c.2241+8_2241+9insAATAGATA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,318,344 control chromosomes in the GnomAD database, including 50,681 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 5089 hom., cov: 0)

Exomes 𝑓: 0.18 ( 45592 hom. )

Consequence

MROH2B
NM_173489.5 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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: Benign. The variant received -10 ACMG points.

BP6

Variant 5-41033829-C-CTATCTATT is Benign according to our data. Variant chr5-41033829-C-CTATCTATT is described in ClinVar as Benign. ClinVar VariationId is 403104.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

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+9insAATAGATA		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+9insAATAGATA	splice_region intron	N/A	ENSP00000382476.4	Q7Z745-1
MROH2B	ENST00000506092.6	TSL:2	c.906+8_906+9insAATAGATA	splice_region intron	N/A	ENSP00000441504.1	F5GZ06
MROH2B	ENST00000503890.5	TSL:2	n.1203+8_1203+9insAATAGATA	splice_region intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.244

AC:

35535

AN:

145896

Hom.:

5087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.270

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.289

GnomAD2 exomes

AF:

0.203

AC:

26860

AN:

132376

AF XY:

0.198

show subpopulations

Gnomad AFR exome

AF:

0.117

Gnomad AMR exome

AF:

0.219

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.118

Gnomad FIN exome

AF:

0.249

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.207

GnomAD4 exome

AF:

0.183

AC:

214323

AN:

1172334

Hom.:

45592

Cov.:

AF XY:

0.187

AC XY:

109235

AN XY:

583400

show subpopulations

African (AFR)

AF:

0.0988

AC:

2723

AN:

27570

American (AMR)

AF:

0.233

AC:

7601

AN:

32572

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

5064

AN:

22074

East Asian (EAS)

AF:

0.123

AC:

4247

AN:

34652

South Asian (SAS)

AF:

0.181

AC:

12725

AN:

70264

European-Finnish (FIN)

AF:

0.263

AC:

12378

AN:

46982

Middle Eastern (MID)

AF:

0.200

AC:

1022

AN:

5100

European-Non Finnish (NFE)

AF:

0.180

AC:

159073

AN:

882956

Other (OTH)

AF:

0.189

AC:

9490

AN:

50164

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

4457

8914

13372

17829

22286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3140

6280

9420

12560

15700

<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:

0.243

AC:

35551

AN:

146010

Hom.:

5089

Cov.:

AF XY:

0.244

AC XY:

17348

AN XY:

71222

show subpopulations

African (AFR)

AF:

0.147

AC:

5714

AN:

38938

American (AMR)

AF:

0.295

AC:

4319

AN:

14644

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

920

AN:

3336

East Asian (EAS)

AF:

0.148

AC:

744

AN:

5044

South Asian (SAS)

AF:

0.236

AC:

1080

AN:

4572

European-Finnish (FIN)

AF:

0.276

AC:

2777

AN:

10056

Middle Eastern (MID)

AF:

0.252

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.287

AC:

19041

AN:

66262

Other (OTH)

AF:

0.287

AC:

575

AN:

2002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1193

2387

3580

4774

5967

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.212

Hom.:

640

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.24

Mutation Taster

=100/0

polymorphism (auto)

(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