dbSNP rs9346: OSER1:p.Val74Gly (chr20-44197710-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_016470.8(OSER1):c.221T>G(p.Val74Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,608,734 control chromosomes in the GnomAD database, including 34,241 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 7546 hom., cov: 32)

Exomes 𝑓: 0.17 ( 26695 hom. )

Consequence

OSER1
NM_016470.8 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.961

Publications

31 publications found

Variant links:

Genes affected

OSER1 (HGNC:16105): (oxidative stress responsive serine rich 1) Predicted to be involved in cellular response to hydrogen peroxide. [provided by Alliance of Genome Resources, Apr 2022]

OSER1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_016470.8, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=3.0824542E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016470.8. 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
	OSER1	NM_016470.8	MANE Select	c.221T>G	p.Val74Gly	missense	Exon 4 of 4	NP_057554.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OSER1	ENST00000255174.3	TSL:1 MANE Select	c.221T>G	p.Val74Gly	missense	Exon 4 of 4	ENSP00000255174.2	Q9NX31
OSER1	ENST00000882657.1		c.338T>G	p.Val113Gly	missense	Exon 5 of 5	ENSP00000552716.1
OSER1	ENST00000372970.6	TSL:3	c.221T>G	p.Val74Gly	missense	Exon 6 of 6	ENSP00000362061.1	Q9NX31

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40241

AN:

151980

Hom.:

7528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.219

GnomAD2 exomes

AF:

0.215

AC:

53983

AN:

251188

AF XY:

0.216

show subpopulations

Gnomad AFR exome

AF:

0.526

Gnomad AMR exome

AF:

0.128

Gnomad ASJ exome

AF:

0.172

Gnomad EAS exome

AF:

0.430

Gnomad FIN exome

AF:

0.185

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.168

AC:

244680

AN:

1456634

Hom.:

26695

Cov.:

AF XY:

0.172

AC XY:

124933

AN XY:

724884

show subpopulations

African (AFR)

AF:

0.528

AC:

17588

AN:

33294

American (AMR)

AF:

0.130

AC:

5817

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

4483

AN:

26088

East Asian (EAS)

AF:

0.429

AC:

17013

AN:

39652

South Asian (SAS)

AF:

0.331

AC:

28491

AN:

86068

European-Finnish (FIN)

AF:

0.193

AC:

10329

AN:

53388

Middle Eastern (MID)

AF:

0.200

AC:

1149

AN:

5744

European-Non Finnish (NFE)

AF:

0.134

AC:

148050

AN:

1107532

Other (OTH)

AF:

0.195

AC:

11760

AN:

60160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.447

Heterozygous variant carriers

8462

16924

25385

33847

42309

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5682

11364

17046

22728

28410

<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:

0.265

AC:

40299

AN:

152100

Hom.:

7546

Cov.:

AF XY:

0.267

AC XY:

19879

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.518

AC:

21441

AN:

41428

American (AMR)

AF:

0.152

AC:

2318

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

628

AN:

3472

East Asian (EAS)

AF:

0.422

AC:

2183

AN:

5178

South Asian (SAS)

AF:

0.335

AC:

1615

AN:

4818

European-Finnish (FIN)

AF:

0.177

AC:

1871

AN:

10600

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9617

AN:

68002

Other (OTH)

AF:

0.219

AC:

463

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1312

2623

3935

5246

6558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.180

Hom.:

13077

Bravo

AF:

0.273

Asia WGS

AF:

0.352

AC:

1225

AN:

3478

EpiCase

AF:

0.145

EpiControl

AF:

0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.048

Eigen

Benign

-0.35

Eigen_PC

Benign

-0.28

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.61

MetaRNN

Benign

0.00031

MetaSVM

Benign

-0.94

MutationAssessor

Benign

2.0

PhyloP100

0.96

PrimateAI

Benign

0.39

PROVEAN

Benign

-1.9

REVEL

Benign

0.036

Sift

Uncertain

0.018

Sift4G

Benign

0.17

Varity_R

0.11

gMVP

0.19

Mutation Taster

=96/4

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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