rs4488102

chr10-23113386-A-Gchr10-23113386-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012228.4(MSRB2):c.296+3068A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,112 control chromosomes in the GnomAD database, including 61,969 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 0.90 (61969 hom., cov: 31)
• Consequence: MSRB2 NM_012228.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSRB2	NM_012228.4	c.296+3068A>G		intron_variant		ENST00000376510.8
MSRB2	XM_011519426.3	c.296+3068A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSRB2	ENST00000376510.8	c.296+3068A>G		intron_variant		1	NM_012228.4	P1
	ENST00000655462.1	n.116+20303T>C		intron_variant, non_coding_transcript_variant
MSRB2	ENST00000472663.1	c.178+3068A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136468 AN: 151994 Hom.: 61930 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.898

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.898 AC: 136559 AN: 152112 Hom.: 61969 Cov.: 31 AF XY: 0.893 AC XY: 66427 AN XY: 74366

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.900

Alfa AF: 0.932 Hom.: 7722

Bravo AF: 0.884

Asia WGS AF: 0.727 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.23
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs4488102; hg19: chr10-23402315;