2-42763238-A-G

Position:

• chr2-42763238-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BS1 BS2

The NM_148962.5(OXER1):​c.825T>C​(p.Phe275Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00225 in 1,612,004 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.012 (36 hom., cov: 33)
  • Exomes 𝑓: 0.0012 (29 hom.)
• Consequence: OXER1 NM_148962.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.53

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]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 2-42763238-A-G is Benign according to our data. Variant chr2-42763238-A-G is described in ClinVar as [Benign]. Clinvar id is 791116.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-1.53 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0119 (1812/152352) while in subpopulation AFR AF= 0.0413 (1717/41588). AF 95% confidence interval is 0.0397. There are 36 homozygotes in gnomad4. There are 877 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXER1	NM_148962.5	c.825T>C	p.Phe275Phe	synonymous_variant	1/1	ENST00000378661.4	NP_683765.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXER1	ENST00000378661.4	c.825T>C	p.Phe275Phe	synonymous_variant	1/1	6	NM_148962.5	ENSP00000367930.3

Frequencies

GnomAD3 genomes AF: 0.0119 AC: 1808 AN: 152234 Hom.: 36 Cov.: 33

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00458

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.00718

GnomAD3 exomes AF: 0.00312 AC: 762 AN: 244056 Hom.: 9 AF XY: 0.00237 AC XY: 314 AN XY: 132492

Gnomad AFR exome AF: 0.0438

Gnomad AMR exome AF: 0.00165

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000133

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000455

Gnomad OTH exome AF: 0.00184

GnomAD4 exome AF: 0.00125 AC: 1821 AN: 1459652 Hom.: 29 Cov.: 38 AF XY: 0.00106 AC XY: 768 AN XY: 725974

Gnomad4 AFR exome AF: 0.0437

Gnomad4 AMR exome AF: 0.00183

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000105

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000837

Gnomad4 OTH exome AF: 0.00265

GnomAD4 genome AF: 0.0119 AC: 1812 AN: 152352 Hom.: 36 Cov.: 33 AF XY: 0.0118 AC XY: 877 AN XY: 74504

Gnomad4 AFR AF: 0.0413

Gnomad4 AMR AF: 0.00457

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.00710

Alfa AF: 0.00453 Hom.: 6

Bravo AF: 0.0131

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 15, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.71

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

Other links and lift over

dbSNP: rs77519354; hg19: chr2-42990378;