10-23111063-T-C

Variant names:

• chr10-23111063-T-C
• rs10764383
• NM_012228.4:c.296+745T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012228.4(MSRB2):​c.296+745T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,250 control chromosomes in the GnomAD database, including 64,508 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 0.92 (64508 hom., cov: 32)
• Consequence: MSRB2 NM_012228.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890
• Publications: 3 publications found

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]

ENSG00000286924 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012228.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSRB2	NM_012228.4	MANE Select	c.296+745T>C		intron	N/A	NP_036360.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSRB2	ENST00000376510.8	TSL:1 MANE Select	c.296+745T>C		intron	N/A	ENSP00000365693.3	Q9Y3D2
	MSRB2	ENST00000900184.1		c.296+745T>C		intron	N/A	ENSP00000570243.1
	MSRB2	ENST00000900183.1		c.296+745T>C		intron	N/A	ENSP00000570242.1

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139334 AN: 152132 Hom.: 64454 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.916 AC: 139445 AN: 152250 Hom.: 64508 Cov.: 32 AF XY: 0.910 AC XY: 67733 AN XY: 74434

African (AFR) AF: 0.921 AC: 38259 AN: 41556

American (AMR) AF: 0.849 AC: 12983 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3319 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2554 AN: 5136

South Asian (SAS) AF: 0.818 AC: 3946 AN: 4822

European-Finnish (FIN) AF: 0.949 AC: 10081 AN: 10622

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65229 AN: 68028

Other (OTH) AF: 0.914 AC: 1932 AN: 2114

Alfa AF: 0.935 Hom.: 15188

Bravo AF: 0.905

Asia WGS AF: 0.725 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	15
DANN	Benign	0.74
PhyloP100		0.89
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10764383; hg19: chr10-23399992;