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

Variant summary

Our verdict is Benign. Variant got -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

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 -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 id 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.

Transcripts

RefSeq

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

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

GnomAD3 exomes

AF:

0.203

AC:

26860

AN:

132376

Hom.:

5287

AF XY:

0.198

AC XY:

13932

AN XY:

70404

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 SAS exome

AF:

0.163

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

Gnomad4 AFR exome

AF:

0.0988

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.229

Gnomad4 EAS exome

AF:

0.123

Gnomad4 SAS exome

AF:

0.181

Gnomad4 FIN exome

AF:

0.263

Gnomad4 NFE exome

AF:

0.180

Gnomad4 OTH exome

AF:

0.189

GnomAD4 genome

AF:

0.243

AC:

35551

AN:

146010

Hom.:

5089

Cov.:

AF XY:

0.244

AC XY:

17348

AN XY:

71222

show subpopulations

Gnomad4 AFR

AF:

0.147

Gnomad4 AMR

AF:

0.295

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.148

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.276

Gnomad4 NFE

AF:

0.287

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.212

Hom.:

640

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Outside splice consensus. -

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over