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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_173489.5(MROH2B):c.2241+8_2241+9insAATAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,178,452 control chromosomes in the GnomAD database, including 511 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.018 ( 47 hom., cov: 0)

Exomes 𝑓: 0.013 ( 511 hom. )

Failed GnomAD Quality Control

Consequence

MROH2B
NM_173489.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.238

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 made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1

Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0131 (15463/1178452) while in subpopulation AMR AF= 0.0369 (1209/32764). AF 95% confidence interval is 0.0352. There are 511 homozygotes in gnomad4_exome. There are 8060 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 511 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
MROH2B	NM_173489.5 link	c.2241+8_2241+9insAATAA	splice_region_variant, intron_variant	Intron 22 of 41	ENST00000399564.5	NP_775760.3
MROH2B	XM_011513952.2 link	c.2241+8_2241+9insAATAA	splice_region_variant, intron_variant	Intron 22 of 42		XP_011512254.1
MROH2B	XM_011513953.2 link	c.2055+8_2055+9insAATAA	splice_region_variant, intron_variant	Intron 21 of 40		XP_011512255.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MROH2B	ENST00000399564.5 link	c.2241+8_2241+9insAATAA	splice_region_variant, intron_variant	Intron 22 of 41	1	NM_173489.5	ENSP00000382476.4	Q7Z745-1
MROH2B	ENST00000506092.6 link	c.906+8_906+9insAATAA	splice_region_variant, intron_variant	Intron 12 of 31	2		ENSP00000441504.1	F5GZ06
MROH2B	ENST00000503890.5 link	n.1203+8_1203+9insAATAA	splice_region_variant, intron_variant	Intron 10 of 30	2
MROH2B	ENST00000515297.5 link	n.1629+8_1629+9insAATAA	splice_region_variant, intron_variant	Intron 16 of 35	5

Frequencies

GnomAD3 genomes

AF:

0.0184

AC:

2690

AN:

146052

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00489

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0310

Gnomad ASJ

AF:

0.00659

Gnomad EAS

AF:

0.000198

Gnomad SAS

AF:

0.0181

Gnomad FIN

AF:

0.0209

Gnomad MID

AF:

0.00987

Gnomad NFE

AF:

0.0255

Gnomad OTH

AF:

0.0161

GnomAD3 exomes

AF:

0.0189

AC:

2497

AN:

132376

Hom.:

AF XY:

0.0187

AC XY:

1314

AN XY:

70404

show subpopulations

Gnomad AFR exome

AF:

0.00404

Gnomad AMR exome

AF:

0.0358

Gnomad ASJ exome

AF:

0.00310

Gnomad EAS exome

AF:

0.0000987

Gnomad SAS exome

AF:

0.0160

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.0210

Gnomad OTH exome

AF:

0.0197

GnomAD4 exome

AF:

0.0131

AC:

15463

AN:

1178452

Hom.:

511

Cov.:

AF XY:

0.0137

AC XY:

8060

AN XY:

586674

show subpopulations

Gnomad4 AFR exome

AF:

0.00279

Gnomad4 AMR exome

AF:

0.0369

Gnomad4 ASJ exome

AF:

0.00351

Gnomad4 EAS exome

AF:

0.0000287

Gnomad4 SAS exome

AF:

0.0188

Gnomad4 FIN exome

AF:

0.0204

Gnomad4 NFE exome

AF:

0.0125

Gnomad4 OTH exome

AF:

0.0136

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0184

AC:

2690

AN:

146166

Hom.:

Cov.:

AF XY:

0.0179

AC XY:

1276

AN XY:

71298

show subpopulations

Gnomad4 AFR

AF:

0.00488

Gnomad4 AMR

AF:

0.0311

Gnomad4 ASJ

AF:

0.00659

Gnomad4 EAS

AF:

0.000198

Gnomad4 SAS

AF:

0.0179

Gnomad4 FIN

AF:

0.0209

Gnomad4 NFE

AF:

0.0255

Gnomad4 OTH

AF:

0.0154

Alfa

AF:

0.0120

Hom.:

640

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over