Variant 5-41033829-C-CTATCTATCTATT details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_173489.5(MROH2B):c.2241+8_2241+9insAATAGATAGATA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 1,177,910 control chromosomes in the GnomAD database, including 4,427 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.038 ( 181 hom., cov: 0)

Exomes 𝑓: 0.026 ( 4427 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 = 0.0259 (30544/1177910) while in subpopulation AMR AF= 0.0317 (1037/32750). AF 95% confidence interval is 0.0301. There are 4427 homozygotes in gnomad4_exome. There are 15468 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 4427 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
MROH2B	NM_173489.5 link	c.2241+8_2241+9insAATAGATAGATA	splice_region_variant, intron_variant	Intron 22 of 41	ENST00000399564.5	NP_775760.3
MROH2B	XM_011513952.2 link	c.2241+8_2241+9insAATAGATAGATA	splice_region_variant, intron_variant	Intron 22 of 42		XP_011512254.1
MROH2B	XM_011513953.2 link	c.2055+8_2055+9insAATAGATAGATA	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+9insAATAGATAGATA	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+9insAATAGATAGATA	splice_region_variant, intron_variant	Intron 12 of 31	2		ENSP00000441504.1	F5GZ06
MROH2B	ENST00000503890.5 link	n.1203+8_1203+9insAATAGATAGATA	splice_region_variant, intron_variant	Intron 10 of 30	2
MROH2B	ENST00000515297.5 link	n.1629+8_1629+9insAATAGATAGATA	splice_region_variant, intron_variant	Intron 16 of 35	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

5565

AN:

146018

Hom.:

180

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0216

Gnomad AMI

AF:

0.0434

Gnomad AMR

AF:

0.0449

Gnomad ASJ

AF:

0.0486

Gnomad EAS

AF:

0.0243

Gnomad SAS

AF:

0.0319

Gnomad FIN

AF:

0.0528

Gnomad MID

AF:

0.0329

Gnomad NFE

AF:

0.0450

Gnomad OTH

AF:

0.0372

GnomAD3 exomes

AF:

0.0294

AC:

3886

AN:

132376

Hom.:

484

AF XY:

0.0280

AC XY:

1970

AN XY:

70404

show subpopulations

Gnomad AFR exome

AF:

0.0160

Gnomad AMR exome

AF:

0.0270

Gnomad ASJ exome

AF:

0.0334

Gnomad EAS exome

AF:

0.0134

Gnomad SAS exome

AF:

0.0209

Gnomad FIN exome

AF:

0.0476

Gnomad NFE exome

AF:

0.0327

Gnomad OTH exome

AF:

0.0291

GnomAD4 exome

AF:

0.0259

AC:

30544

AN:

1177910

Hom.:

4427

Cov.:

AF XY:

0.0264

AC XY:

15468

AN XY:

586402

show subpopulations

Gnomad4 AFR exome

AF:

0.0144

Gnomad4 AMR exome

AF:

0.0317

Gnomad4 ASJ exome

AF:

0.0389

Gnomad4 EAS exome

AF:

0.0141

Gnomad4 SAS exome

AF:

0.0237

Gnomad4 FIN exome

AF:

0.0487

Gnomad4 NFE exome

AF:

0.0251

Gnomad4 OTH exome

AF:

0.0280

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0381

AC:

5573

AN:

146132

Hom.:

181

Cov.:

AF XY:

0.0385

AC XY:

2746

AN XY:

71282

show subpopulations

Gnomad4 AFR

AF:

0.0216

Gnomad4 AMR

AF:

0.0450

Gnomad4 ASJ

AF:

0.0486

Gnomad4 EAS

AF:

0.0248

Gnomad4 SAS

AF:

0.0317

Gnomad4 FIN

AF:

0.0528

Gnomad4 NFE

AF:

0.0450

Gnomad4 OTH

AF:

0.0388

Alfa

AF:

0.0327

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