Variant chr2-42763085-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_148962.5(OXER1):c.978G>C(p.Gln326His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00545 in 1,614,148 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0039 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0056 ( 31 hom. )

Consequence

OXER1
NM_148962.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0190

Variant links:

Genes affected

OXER1 (HGNC:24884): (oxoeicosanoid receptor 1) Enables G protein-coupled receptor activity and icosanoid binding activity. Involved in adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

OXER1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0049654245).

BP6

Variant 2-42763085-C-G is Benign according to our data. Variant chr2-42763085-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3341549.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-42763085-C-G is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXER1	NM_148962.5 linkuse as main transcript	c.978G>C	p.Gln326His	missense_variant	1/1	ENST00000378661.4	NP_683765.2	Q8TDS5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXER1	ENST00000378661.4 linkuse as main transcript	c.978G>C	p.Gln326His	missense_variant	1/1	6	NM_148962.5	ENSP00000367930.3		Q8TDS5

Frequencies

GnomAD3 genomes

AF:

0.00393

AC:

598

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000989

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00641

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00645

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00374

AC:

936

AN:

250282

Hom.:

AF XY:

0.00363

AC XY:

492

AN XY:

135680

show subpopulations

Gnomad AFR exome

AF:

0.000955

Gnomad AMR exome

AF:

0.00448

Gnomad ASJ exome

AF:

0.00109

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000196

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00638

Gnomad OTH exome

AF:

0.00378

GnomAD4 exome

AF:

0.00560

AC:

8193

AN:

1461822

Hom.:

Cov.:

AF XY:

0.00544

AC XY:

3958

AN XY:

727220

show subpopulations

Gnomad4 AFR exome

AF:

0.000956

Gnomad4 AMR exome

AF:

0.00436

Gnomad4 ASJ exome

AF:

0.00111

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000278

Gnomad4 FIN exome

AF:

0.000300

Gnomad4 NFE exome

AF:

0.00686

Gnomad4 OTH exome

AF:

0.00435

GnomAD4 genome

AF:

0.00393

AC:

598

AN:

152326

Hom.:

Cov.:

AF XY:

0.00360

AC XY:

268

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.000986

Gnomad4 AMR

AF:

0.00640

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00645

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.00532

Hom.:

Bravo

AF:

0.00434

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00649

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00500

AC:

ExAC

AF:

0.00344

AC:

417

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00627

EpiControl

AF:

0.00664

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

Aug 01, 2024

OXER1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0041

Eigen

Benign

-0.32

Eigen_PC

Benign

-0.42

FATHMM_MKL

Benign

0.22

LIST_S2

Benign

0.48

M_CAP

Benign

0.0031

MetaRNN

Benign

0.0050

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.69

PrimateAI

Benign

0.33

PROVEAN

Benign

-1.4

REVEL

Benign

0.096

Sift

Benign

0.52

Sift4G

Uncertain

0.043

Polyphen

0.99

Vest4

0.29

MutPred

0.48

Gain of catalytic residue at Q365 (P = 0.0315);

MVP

0.61

MPC

0.21

ClinPred

0.012

GERP RS

3.1

Varity_R

0.14

gMVP

0.24

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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