rs13331553

chr16-1940993-T-C

Variant summary

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

The NM_016332.4(MSRB1):c.205-101A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 1,573,354 control chromosomes in the GnomAD database, including 84,339 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 0.37 (11659 hom., cov: 32)
  • Exomes 𝑓: 0.31 (72680 hom.)
• Consequence: MSRB1 NM_016332.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

MSRB1 (HGNC:14133): (methionine sulfoxide reductase B1) The protein encoded by this gene belongs to the methionine-R-sulfoxide reductase B (MsrB) family. Members of this family function as repair enzymes that protect proteins from oxidative stress by catalyzing the reduction of methionine-R-sulfoxides to methionines. This protein is highly expressed in liver and kidney, and is localized to the nucleus and cytosol. It is the only member of the MsrB family that is a selenoprotein, containing a selenocysteine (Sec) residue at its active site. It also has the highest methionine-R-sulfoxide reductase activity compared to other members containing cysteine in place of Sec. Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. A pseudogene of this locus has been identified on chromosome 19. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=2.6244059E-5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSRB1	NM_016332.4	c.205-101A>G		intron_variant		ENST00000361871.8
MSRB1	NM_001382264.1	c.173-101A>G		intron_variant
MSRB1	NM_001382265.1	c.204+264A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSRB1	ENST00000361871.8	c.205-101A>G		intron_variant		1	NM_016332.4	P1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56125 AN: 151902 Hom.: 11641 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.348

GnomAD3 exomes AF: 0.335 AC: 61708 AN: 184176 Hom.: 11599 AF XY: 0.345 AC XY: 34313 AN XY: 99362

Gnomad AFR exome AF: 0.561

Gnomad AMR exome AF: 0.173

Gnomad ASJ exome AF: 0.376

Gnomad EAS exome AF: 0.531

Gnomad SAS exome AF: 0.484

Gnomad FIN exome AF: 0.279

Gnomad NFE exome AF: 0.289

Gnomad OTH exome AF: 0.311

GnomAD4 exome AF: 0.308 AC: 438401 AN: 1421332 Hom.: 72680 Cov.: 78 AF XY: 0.314 AC XY: 220787 AN XY: 703562

Gnomad4 AFR exome AF: 0.563

Gnomad4 AMR exome AF: 0.178

Gnomad4 ASJ exome AF: 0.376

Gnomad4 EAS exome AF: 0.581

Gnomad4 SAS exome AF: 0.478

Gnomad4 FIN exome AF: 0.277

Gnomad4 NFE exome AF: 0.282

Gnomad4 OTH exome AF: 0.329

GnomAD4 genome AF: 0.370 AC: 56189 AN: 152022 Hom.: 11659 Cov.: 32 AF XY: 0.369 AC XY: 27407 AN XY: 74284

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.350

Alfa AF: 0.288 Hom.: 8860

Bravo AF: 0.370

TwinsUK AF: 0.284 AC: 1053

ALSPAC AF: 0.271 AC: 1043

ExAC AF: 0.305 AC: 34978

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.50	T
BayesDel_noAF	Benign	-0.35
Cadd	Benign	8.7
Dann	Benign	0.40
Eigen	Benign	-0.98
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.0029	N
LIST_S2	Benign	0.18	T
MetaRNN	Benign	0.000026	T
MetaSVM	Benign	-0.96	T
MutationTaster	Benign	1.0	P;P;P
PROVEAN	Benign	0.0	N
REVEL	Benign	0.082
Sift	Pathogenic	0.0	D
Vest4		0.051
ClinPred		0.012	T
GERP RS		-2.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs13331553; hg19: chr16-1990994; COSMIC: COSV51907767; COSMIC: COSV51907767;