rs10487133

chr7-95406638-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_000305.3(PON2):c.777+349C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,192 control chromosomes in the GnomAD database, including 56,658 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 0.86 (56658 hom., cov: 32)
• Consequence: PON2 NM_000305.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746

Genes affected

PON2 (HGNC:9205): (paraoxonase 2) This gene encodes a member of the paraoxonase gene family, which includes three known members located adjacent to each other on the long arm of chromosome 7. The encoded protein is ubiquitously expressed in human tissues, membrane-bound, and may act as a cellular antioxidant, protecting cells from oxidative stress. Hydrolytic activity against acylhomoserine lactones, important bacterial quorum-sensing mediators, suggests the encoded protein may also play a role in defense responses to pathogenic bacteria. Mutations in this gene may be associated with vascular disease and a number of quantitative phenotypes related to diabetes. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

LOC107986822 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PON2	NM_000305.3	c.777+349C>A		intron_variant		ENST00000222572.8
LOC107986822	XR_007060439.1	n.557+9610G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PON2	ENST00000222572.8	c.777+349C>A		intron_variant		1	NM_000305.3	P1

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131113 AN: 152074 Hom.: 56613 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.868

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.862 AC: 131217 AN: 152192 Hom.: 56658 Cov.: 32 AF XY: 0.866 AC XY: 64428 AN XY: 74412

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.870

Alfa AF: 0.878 Hom.: 79056

Bravo AF: 0.857

Asia WGS AF: 0.863 AC: 3002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	17
Dann	Benign	0.77

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

Other links and lift over

dbSNP: rs10487133; hg19: chr7-95035950;