rs11013295

chr10-23115825-A-Gchr10-23115825-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.297-3479A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,022 control chromosomes in the GnomAD database, including 33,931 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 0.66 (33931 hom., cov: 32)
• Consequence: MSRB2 NM_012228.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

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=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSRB2	NM_012228.4	c.297-3479A>G		intron_variant		ENST00000376510.8
MSRB2	XM_011519426.3	c.297-3221A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSRB2	ENST00000376510.8	c.297-3479A>G		intron_variant		1	NM_012228.4	P1
	ENST00000655462.1	n.116+17864T>C		intron_variant, non_coding_transcript_variant
MSRB2	ENST00000472663.1	c.179-3221A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100808 AN: 151904 Hom.: 33905 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.663 AC: 100866 AN: 152022 Hom.: 33931 Cov.: 32 AF XY: 0.657 AC XY: 48826 AN XY: 74314

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.646

Alfa AF: 0.662 Hom.: 6583

Bravo AF: 0.667

Asia WGS AF: 0.479 AC: 1664 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	13
Dann	Benign	0.70

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: rs11013295; hg19: chr10-23404754;