GeneBe

rs3917525

Positions:

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000446.7(PON1):​c.497+284delC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6164 hom., cov: 20)

Consequence

PON1
NM_000446.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0300
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 7-95311166-TG-T is Benign according to our data. Variant chr7-95311166-TG-T is described in ClinVar as [Benign]. Clinvar id is 1239123.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PON1NM_000446.7 linkuse as main transcriptc.497+284delC intron_variant ENST00000222381.8 NP_000437.3 P27169

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PON1ENST00000222381.8 linkuse as main transcriptc.497+284delC intron_variant 1 NM_000446.7 ENSP00000222381.3 P27169
PON1ENST00000433729.1 linkuse as main transcriptn.*222+284delC intron_variant 3 ENSP00000407359.1 F8WF42

Frequencies

GnomAD3 genomes
AF:
0.277
AC:
42077
AN:
151856
Hom.:
6142
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.364
Gnomad AMI
AF:
0.299
Gnomad AMR
AF:
0.268
Gnomad ASJ
AF:
0.251
Gnomad EAS
AF:
0.505
Gnomad SAS
AF:
0.265
Gnomad FIN
AF:
0.219
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.220
Gnomad OTH
AF:
0.280
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.277
AC:
42135
AN:
151974
Hom.:
6164
Cov.:
20
AF XY:
0.279
AC XY:
20690
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.364
Gnomad4 AMR
AF:
0.268
Gnomad4 ASJ
AF:
0.251
Gnomad4 EAS
AF:
0.505
Gnomad4 SAS
AF:
0.265
Gnomad4 FIN
AF:
0.219
Gnomad4 NFE
AF:
0.220
Gnomad4 OTH
AF:
0.287
Alfa
AF:
0.243
Hom.:
569
Bravo
AF:
0.286
Asia WGS
AF:
0.406
AC:
1408
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3917525; hg19: chr7-94940478; API