rs11013295

Variant names:

• chr10-23115825-A-G
• rs11013295
• NM_012228.4:c.297-3479A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-23115825-A-G
• chr10-23115825-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.57).
• 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 rank	MANE	Protein	UniProt
MSRB2	NM_012228.4	c.297-3479A>G		intron_variant	Intron 3 of 4	ENST00000376510.8	NP_036360.3
MSRB2	XM_011519426.3	c.297-3221A>G		intron_variant	Intron 3 of 3		XP_011517728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRB2	ENST00000376510.8	c.297-3479A>G		intron_variant	Intron 3 of 4	1	NM_012228.4	ENSP00000365693.3
MSRB2	ENST00000472663.1	n.177-3221A>G		intron_variant	Intron 2 of 4	5		ENSP00000434990.1
ENSG00000286924	ENST00000655462.1	n.116+17864T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.718 AC: 29758 AN: 41442

American (AMR) AF: 0.642 AC: 9811 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2487 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1744 AN: 5164

South Asian (SAS) AF: 0.558 AC: 2696 AN: 4828

European-Finnish (FIN) AF: 0.618 AC: 6508 AN: 10534

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45695 AN: 67980

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.664 Hom.: 6789

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
PhyloP100		0.38
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: rs11013295; hg19: chr10-23404754;