rs6601427

Variant names:

• chr8-10298515-T-C
• rs6601427
• NM_012331.5:c.332-3019T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-10298515-T-C
• chr8-10298515-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012331.5(MSRA):​c.332-3019T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,930 control chromosomes in the GnomAD database, including 22,092 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 0.52 (22092 hom., cov: 31)
• Consequence: MSRA NM_012331.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSRA	NM_012331.5	c.332-3019T>C		intron_variant	Intron 3 of 5	ENST00000317173.9	NP_036463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRA	ENST00000317173.9	c.332-3019T>C		intron_variant	Intron 3 of 5	1	NM_012331.5	ENSP00000313921.4

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79280 AN: 151810 Hom.: 22062 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.522 AC: 79345 AN: 151930 Hom.: 22092 Cov.: 31 AF XY: 0.508 AC XY: 37722 AN XY: 74266

African (AFR) AF: 0.616 AC: 25519 AN: 41398

American (AMR) AF: 0.378 AC: 5774 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2101 AN: 3468

East Asian (EAS) AF: 0.00793 AC: 41 AN: 5170

South Asian (SAS) AF: 0.376 AC: 1804 AN: 4800

European-Finnish (FIN) AF: 0.417 AC: 4401 AN: 10564

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37919 AN: 67948

Other (OTH) AF: 0.523 AC: 1105 AN: 2114

Alfa AF: 0.522 Hom.: 10173

Bravo AF: 0.520

Asia WGS AF: 0.239 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.32
PhyloP100		0.0070
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: rs6601427; hg19: chr8-10156025;