Variant chr7-95308475-CGTGTGT-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000446.7(PON1):c.498-270_498-265del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1142 hom., cov: 0)

Consequence

PON1
NM_000446.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

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]

PON1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-95308475-CGTGTGT-C is Benign according to our data. Variant chr7-95308475-CGTGTGT-C is described in ClinVar as [Benign]. Clinvar id is 1273749.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PON1	NM_000446.7 linkuse as main transcript	c.498-270_498-265del		intron_variant		ENST00000222381.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PON1	ENST00000222381.8 linkuse as main transcript	c.498-270_498-265del		intron_variant		1	NM_000446.7	P1
PON1	ENST00000433729.1 linkuse as main transcript	c.223-270_223-265del		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

18537

AN:

146964

Hom.:

1141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0861

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.111

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

GnomAD4 genome

AF:

0.126

AC:

18559

AN:

147072

Hom.:

1142

Cov.:

AF XY:

0.128

AC XY:

9141

AN XY:

71512

show subpopulations

Gnomad4 AFR

AF:

0.113

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.0861

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.101

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.129

Gnomad4 OTH

AF:

0.114

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 submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over