Variant 10-23119349-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_012228.4(MSRB2):c.342C>T(p.Ser114Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,613,762 control chromosomes in the GnomAD database, including 85,085 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 0.29 ( 6597 hom., cov: 31)

Exomes 𝑓: 0.32 ( 78488 hom. )

Consequence

MSRB2
NM_012228.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.05

Variant links:

Genes affected

MSRB2 (HGNC:17061): (methionine sulfoxide reductase B2) Predicted to enable actin binding activity; peptide-methionine (R)-S-oxide reductase activity; and zinc ion binding activity. Predicted to be involved in actin filament polymerization and protein repair. Predicted to be located in mitochondrion. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MSRB2 links:

MSRB2 (HGNC:):

MSRB2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP7

Synonymous conserved (PhyloP=-3.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSRB2	NM_012228.4 linkuse as main transcript	c.342C>T	p.Ser114Ser	synonymous_variant	4/5	ENST00000376510.8	NP_036360.3	Q9Y3D2
MSRB2	XM_011519426.3 linkuse as main transcript	c.*174C>T		3_prime_UTR_variant	4/4		XP_011517728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MSRB2	ENST00000376510.8 linkuse as main transcript	c.342C>T	p.Ser114Ser	synonymous_variant	4/5	1	NM_012228.4	ENSP00000365693.3	Q9Y3D2
MSRB2	ENST00000468633.1 linkuse as main transcript	n.206C>T		non_coding_transcript_exon_variant	1/2	2
MSRB2	ENST00000472663.1 linkuse as main transcript	n.311C>T		non_coding_transcript_exon_variant	4/5	5		ENSP00000434990.1	H0YE51
ENSG00000286924	ENST00000655462.1 linkuse as main transcript	n.116+14340G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.287

AC:

43603

AN:

151900

Hom.:

6593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.317

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.257

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.284

AC:

70945

AN:

249376

Hom.:

10755

AF XY:

0.291

AC XY:

39320

AN XY:

135278

show subpopulations

Gnomad AFR exome

AF:

0.242

Gnomad AMR exome

AF:

0.172

Gnomad ASJ exome

AF:

0.319

Gnomad EAS exome

AF:

0.145

Gnomad SAS exome

AF:

0.273

Gnomad FIN exome

AF:

0.325

Gnomad NFE exome

AF:

0.339

Gnomad OTH exome

AF:

0.294

GnomAD4 exome

AF:

0.324

AC:

473051

AN:

1461744

Hom.:

78488

Cov.:

AF XY:

0.324

AC XY:

235480

AN XY:

727170

show subpopulations

Gnomad4 AFR exome

AF:

0.236

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.320

Gnomad4 EAS exome

AF:

0.152

Gnomad4 SAS exome

AF:

0.276

Gnomad4 FIN exome

AF:

0.326

Gnomad4 NFE exome

AF:

0.343

Gnomad4 OTH exome

AF:

0.312

GnomAD4 genome

AF:

0.287

AC:

43625

AN:

152018

Hom.:

6597

Cov.:

AF XY:

0.282

AC XY:

20990

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.317

Gnomad4 EAS

AF:

0.136

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.342

Gnomad4 OTH

AF:

0.261

Alfa

AF:

0.323

Hom.:

19696

Bravo

AF:

0.277

Asia WGS

AF:

0.205

AC:

711

AN:

3478

EpiCase

AF:

0.338

EpiControl

AF:

0.336

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

1.9

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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