rs854568

chr7-95320489-G-A

Variant summary

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

The NM_000446.7(PON1):c.75-2096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,132 control chromosomes in the GnomAD database, including 36,817 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 0.69 (36817 hom., cov: 33)
• Consequence: PON1 NM_000446.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

Genes affected

PON1 (HGNC:9204): (paraoxonase 1) This gene encodes a member of the paraoxonase family of enzymes and exhibits lactonase and ester hydrolase activity. Following synthesis in the kidney and liver, the enzyme is secreted into the circulation, where it binds to high density lipoprotein (HDL) particles and hydrolyzes thiolactones and xenobiotics, including paraoxon, a metabolite of the insecticide parathion. Polymorphisms in this gene may be associated with coronary artery disease and diabetic retinopathy. The gene is found in a cluster of three related paraoxonase genes on chromosome 7. [provided by RefSeq, Aug 2017]

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 (NFE) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PON1	NM_000446.7	c.75-2096C>T		intron_variant		ENST00000222381.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PON1	ENST00000222381.8	c.75-2096C>T		intron_variant		1	NM_000446.7	P1
PON1	ENST00000433729.1	c.75-2096C>T		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104342 AN: 152014 Hom.: 36792 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.686 AC: 104407 AN: 152132 Hom.: 36817 Cov.: 33 AF XY: 0.685 AC XY: 50899 AN XY: 74348

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.719

Alfa AF: 0.756 Hom.: 60277

Bravo AF: 0.683

Asia WGS AF: 0.686 AC: 2390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.73

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: rs854568; hg19: chr7-94949801;