Variant 3-38198789-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_005109.3(OXSR1):c.360A>G(p.Glu120Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0049 in 1,613,082 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0050 ( 32 hom. )

Consequence

OXSR1
NM_005109.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.107

Variant links:

Genes affected

OXSR1 (HGNC:8508): (oxidative stress responsive kinase 1) The product of this gene belongs to the Ser/Thr protein kinase family of proteins. It regulates downstream kinases in response to environmental stress, and may play a role in regulating the actin cytoskeleton. [provided by RefSeq, Jul 2008]

OXSR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 3-38198789-A-G is Benign according to our data. Variant chr3-38198789-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2653668.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.107 with no splicing effect.

BS2

High AC in GnomAd4 at 626 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXSR1	NM_005109.3 link	c.360A>G	p.Glu120Glu	synonymous_variant	4/18	ENST00000311806.8	NP_005100.1	O95747

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
OXSR1	ENST00000311806.8 link	c.360A>G	p.Glu120Glu	synonymous_variant	4/18	1	NM_005109.3	ENSP00000311713.3	O95747
OXSR1	ENST00000426620.5 link	n.*155A>G		non_coding_transcript_exon_variant	5/11	1		ENSP00000398356.1	F8WBK9
OXSR1	ENST00000426620.5 link	n.*155A>G		3_prime_UTR_variant	5/11	1		ENSP00000398356.1	F8WBK9
OXSR1	ENST00000446845.5 link	c.360A>G	p.Glu120Glu	synonymous_variant	4/15	5		ENSP00000415851.1	C9JIG9

Frequencies

GnomAD3 genomes

AF:

0.00413

AC:

628

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000830

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00651

Gnomad OTH

AF:

0.00956

GnomAD3 exomes

AF:

0.00447

AC:

1124

AN:

251248

Hom.:

AF XY:

0.00471

AC XY:

639

AN XY:

135782

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.00532

Gnomad ASJ exome

AF:

0.00993

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000882

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00649

Gnomad OTH exome

AF:

0.00653

GnomAD4 exome

AF:

0.00498

AC:

7279

AN:

1460762

Hom.:

Cov.:

AF XY:

0.00519

AC XY:

3770

AN XY:

726746

show subpopulations

Gnomad4 AFR exome

AF:

0.00248

Gnomad4 AMR exome

AF:

0.00548

Gnomad4 ASJ exome

AF:

0.00926

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000881

Gnomad4 FIN exome

AF:

0.00127

Gnomad4 NFE exome

AF:

0.00553

Gnomad4 OTH exome

AF:

0.00557

GnomAD4 genome

AF:

0.00411

AC:

626

AN:

152320

Hom.:

Cov.:

AF XY:

0.00411

AC XY:

306

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.00431

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000831

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.00651

Gnomad4 OTH

AF:

0.00946

Alfa

AF:

0.00519

Hom.:

Bravo

AF:

0.00421

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00868

EpiControl

AF:

0.00919

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

OXSR1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

3.6

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over