rs10953146

chr7-95394053-A-Cchr7-95394053-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000940.3(PON3):c.145+591T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,820 control chromosomes in the GnomAD database, including 22,670 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 0.54 (22670 hom., cov: 31)
• Consequence: PON3 NM_000940.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

Genes affected

PON3 (HGNC:9206): (paraoxonase 3) This gene is a member of the paraoxonase family and lies in a cluster on chromosome 7 with the other two family members. The encoded protein is secreted into the bloodstream and associates with high-density lipoprotein (HDL). The protein also rapidly hydrolyzes lactones and can inhibit the oxidation of low-density lipoprotein (LDL), a function that is believed to slow the initiation and progression of atherosclerosis. Alternatively spliced variants which encode different protein isoforms have been described; however, only one has been fully characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PON3	NM_000940.3	c.145+591T>G		intron_variant		ENST00000265627.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PON3	ENST00000265627.10	c.145+591T>G		intron_variant		1	NM_000940.3	P1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81837 AN: 151702 Hom.: 22617 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.540 AC: 81948 AN: 151820 Hom.: 22670 Cov.: 31 AF XY: 0.554 AC XY: 41089 AN XY: 74190

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.522

Alfa AF: 0.503 Hom.: 2416

Bravo AF: 0.539

Asia WGS AF: 0.738 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.40

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: rs10953146; hg19: chr7-95023365;