dbSNP rs10098474: MSRA-DT:n.148G>A (chr8-10054107-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000562143.1(MSRA-DT):n.148G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 156,812 control chromosomes in the GnomAD database, including 35,440 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 0.65 ( 34115 hom., cov: 33)

Exomes 𝑓: 0.75 ( 1325 hom. )

Consequence

MSRA-DT
ENST00000562143.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.841

Publications

12 publications found

Variant links:

Genes affected

MSRA-DT (HGNC:55400): (MSRA divergent transcript)

MSRA-DT links:

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]

MSRA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562143.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSRA	NM_012331.5	MANE Select	c.-410C>T		upstream_gene	N/A	NP_036463.1	Q9UJ68-1
	MSRA	NM_001135670.3		c.-410C>T		upstream_gene	N/A	NP_001129142.1	Q9UJ68-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MSRA-DT	ENST00000562143.1	TSL:6	n.148G>A	non_coding_transcript_exon	Exon 1 of 1
MSRA-DT	ENST00000659604.1		n.116+819G>A	intron	N/A
MSRA-DT	ENST00000843173.1		n.32+819G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.655

AC:

99529

AN:

152054

Hom.:

34135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.846

Gnomad AMR

AF:

0.623

Gnomad ASJ

AF:

0.797

Gnomad EAS

AF:

0.598

Gnomad SAS

AF:

0.709

Gnomad FIN

AF:

0.766

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.761

Gnomad OTH

AF:

0.701

GnomAD4 exome

AF:

0.751

AC:

3485

AN:

4640

Hom.:

1325

Cov.:

AF XY:

0.754

AC XY:

1658

AN XY:

2198

show subpopulations

African (AFR)

AF:

0.408

AC:

AN:

152

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.820

AC:

100

AN:

122

East Asian (EAS)

AF:

0.546

AC:

AN:

108

South Asian (SAS)

AF:

0.791

AC:

106

AN:

134

European-Finnish (FIN)

AF:

0.816

AC:

186

AN:

228

Middle Eastern (MID)

AF:

0.625

AC:

AN:

European-Non Finnish (NFE)

AF:

0.771

AC:

2677

AN:

3474

Other (OTH)

AF:

0.727

AC:

263

AN:

362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

118

157

196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.654

AC:

99517

AN:

152172

Hom.:

34115

Cov.:

AF XY:

0.655

AC XY:

48710

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.443

AC:

18374

AN:

41510

American (AMR)

AF:

0.622

AC:

9508

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.797

AC:

2767

AN:

3470

East Asian (EAS)

AF:

0.598

AC:

3086

AN:

5160

South Asian (SAS)

AF:

0.710

AC:

3425

AN:

4824

European-Finnish (FIN)

AF:

0.766

AC:

8109

AN:

10584

Middle Eastern (MID)

AF:

0.786

AC:

231

AN:

294

European-Non Finnish (NFE)

AF:

0.761

AC:

51783

AN:

68012

Other (OTH)

AF:

0.692

AC:

1462

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1627

3254

4881

6508

8135

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.721

Hom.:

63719

Bravo

AF:

0.632

Asia WGS

AF:

0.620

AC:

2155

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

6.3

(source)

DANN

Benign

0.81

PhyloP100

0.84

PromoterAI

-0.024

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over