rs7778771

chr7-95361024-G-A

Variant summary

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

The NM_000940.3(PON3):c.907-893C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0279 in 152,106 control chromosomes in the GnomAD database, including 113 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 0.028 (113 hom., cov: 32)
• Consequence: PON3 NM_000940.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PON3	NM_000940.3	c.907-893C>T		intron_variant		ENST00000265627.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PON3	ENST00000265627.10	c.907-893C>T		intron_variant		1	NM_000940.3	P1

Frequencies

GnomAD3 genomes AF: 0.0278 AC: 4225 AN: 151988 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0175

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00793

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0279 AC: 4250 AN: 152106 Hom.: 113 Cov.: 32 AF XY: 0.0283 AC XY: 2107 AN XY: 74374

Gnomad4 AFR AF: 0.0680

Gnomad4 AMR AF: 0.0174

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.0277

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.00793

Gnomad4 OTH AF: 0.0213

Alfa AF: 0.0209 Hom.: 12

Bravo AF: 0.0288

Asia WGS AF: 0.0410 AC: 144 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.50

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: rs7778771; hg19: chr7-94990336;