Variant rs1001420 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_173489.5(MROH2B):c.4461C>T(p.Tyr1487Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 1,613,428 control chromosomes in the GnomAD database, including 375,532 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.67 ( 33838 hom., cov: 31)

Exomes 𝑓: 0.68 ( 341694 hom. )

Consequence

MROH2B
NM_173489.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

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:

MROH2B (HGNC:):

MROH2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MROH2B	NM_173489.5 linkuse as main transcript	c.4461C>T	p.Tyr1487Tyr	synonymous_variant	39/42	ENST00000399564.5	NP_775760.3
MROH2B	XM_011513952.2 linkuse as main transcript	c.4461C>T	p.Tyr1487Tyr	synonymous_variant	39/43		XP_011512254.1
MROH2B	XM_011513953.2 linkuse as main transcript	c.4275C>T	p.Tyr1425Tyr	synonymous_variant	38/41		XP_011512255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MROH2B	ENST00000399564.5 linkuse as main transcript	c.4461C>T	p.Tyr1487Tyr	synonymous_variant	39/42	1	NM_173489.5	ENSP00000382476.4		Q7Z745-1

Frequencies

GnomAD3 genomes

AF:

0.665

AC:

101016

AN:

151886

Hom.:

33818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.658

Gnomad AMR

AF:

0.627

Gnomad ASJ

AF:

0.655

Gnomad EAS

AF:

0.675

Gnomad SAS

AF:

0.559

Gnomad FIN

AF:

0.736

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.697

Gnomad OTH

AF:

0.668

GnomAD3 exomes

AF:

0.660

AC:

164170

AN:

248640

Hom.:

54731

AF XY:

0.656

AC XY:

88457

AN XY:

134854

show subpopulations

Gnomad AFR exome

AF:

0.619

Gnomad AMR exome

AF:

0.610

Gnomad ASJ exome

AF:

0.660

Gnomad EAS exome

AF:

0.683

Gnomad SAS exome

AF:

0.547

Gnomad FIN exome

AF:

0.734

Gnomad NFE exome

AF:

0.694

Gnomad OTH exome

AF:

0.664

GnomAD4 exome

AF:

0.682

AC:

996895

AN:

1461424

Hom.:

341694

Cov.:

AF XY:

0.678

AC XY:

493194

AN XY:

726988

show subpopulations

Gnomad4 AFR exome

AF:

0.623

Gnomad4 AMR exome

AF:

0.613

Gnomad4 ASJ exome

AF:

0.662

Gnomad4 EAS exome

AF:

0.681

Gnomad4 SAS exome

AF:

0.544

Gnomad4 FIN exome

AF:

0.739

Gnomad4 NFE exome

AF:

0.696

Gnomad4 OTH exome

AF:

0.671

GnomAD4 genome

AF:

0.665

AC:

101089

AN:

152004

Hom.:

33838

Cov.:

AF XY:

0.663

AC XY:

49308

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.620

Gnomad4 AMR

AF:

0.627

Gnomad4 ASJ

AF:

0.655

Gnomad4 EAS

AF:

0.676

Gnomad4 SAS

AF:

0.558

Gnomad4 FIN

AF:

0.736

Gnomad4 NFE

AF:

0.697

Gnomad4 OTH

AF:

0.668

Alfa

AF:

0.681

Hom.:

57887

Bravo

AF:

0.657

Asia WGS

AF:

0.620

AC:

2157

AN:

3478

EpiCase

AF:

0.687

EpiControl

AF:

0.683

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.027

DANN

Benign

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.25

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.25

Position offset: -21

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