rs7132313

Positions:

• chr12-65282462-T-C

Variant summary

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

The NM_001031679.3(MSRB3):​c.-52+3597T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,178 control chromosomes in the GnomAD database, including 1,935 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 0.097 (1935 hom., cov: 32)
• Consequence: MSRB3 NM_001031679.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

Genes affected

MSRB3 (HGNC:27375): (methionine sulfoxide reductase B3) The protein encoded by this gene catalyzes the reduction of methionine sulfoxide to methionine. This enzyme acts as a monomer and requires zinc as a cofactor. Several transcript variants encoding two different isoforms have been found for this gene. One of the isoforms localizes to mitochondria while the other localizes to endoplasmic reticula. [provided by RefSeq, Jul 2010]

MSRB3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSRB3	NM_001031679.3	c.-52+3597T>C		intron_variant		ENST00000308259.10	NP_001026849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSRB3	ENST00000308259.10	c.-52+3597T>C		intron_variant		1	NM_001031679.3	ENSP00000312274.6

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14730 AN: 152060 Hom.: 1927 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.00688

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0971 AC: 14771 AN: 152178 Hom.: 1935 Cov.: 32 AF XY: 0.0954 AC XY: 7101 AN XY: 74444

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.0394

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.0650

Gnomad4 SAS AF: 0.0881

Gnomad4 FIN AF: 0.00688

Gnomad4 NFE AF: 0.0133

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0635 Hom.: 143

Bravo AF: 0.107

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.73
DANN	Benign	0.24

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: rs7132313; hg19: chr12-65676242;