rs17151901

Variant names:

• chr8-10395945-C-T
• rs17151901
• NM_012331.5:c.544-32203C>T

Variant summary

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

The NM_012331.5(MSRA):​c.544-32203C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,196 control chromosomes in the GnomAD database, including 2,258 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 0.11 (2258 hom., cov: 32)
• Consequence: MSRA NM_012331.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

Genes affected

MSRA (HGNC:7377): (methionine sulfoxide reductase A) This gene encodes a ubiquitous and highly conserved protein that carries out the enzymatic reduction of methionine sulfoxide to methionine. Human and animal studies have shown the highest levels of expression in kidney and nervous tissue. The protein functions in the repair of oxidatively damaged proteins to restore biological activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSRA	NM_012331.5	c.544-32203C>T		intron_variant	Intron 5 of 5	ENST00000317173.9	NP_036463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRA	ENST00000317173.9	c.544-32203C>T		intron_variant	Intron 5 of 5	1	NM_012331.5	ENSP00000313921.4

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16429 AN: 152078 Hom.: 2246 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0235

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.108 AC: 16464 AN: 152196 Hom.: 2258 Cov.: 32 AF XY: 0.106 AC XY: 7890 AN XY: 74412

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0477

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0235

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0599 Hom.: 237

Bravo AF: 0.118

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.052
DANN	Benign	0.63

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: rs17151901; hg19: chr8-10253455;