7-95301959-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000446.7(PON1):c.909+246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 148,780 control chromosomes in the GnomAD database, including 937 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.10 ( 937 hom., cov: 25)
Consequence
PON1
NM_000446.7 intron
NM_000446.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.418
Publications
3 publications found
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 Gene-Disease associations (from GenCC):
- amyotrophic lateral sclerosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 7-95301959-T-C is Benign according to our data. Variant chr7-95301959-T-C is described in ClinVar as [Benign]. Clinvar id is 1233629.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PON1 | ENST00000222381.8 | c.909+246A>G | intron_variant | Intron 8 of 8 | 1 | NM_000446.7 | ENSP00000222381.3 | |||
PON1 | ENST00000433729.1 | n.*634+246A>G | intron_variant | Intron 8 of 8 | 3 | ENSP00000407359.1 | ||||
PON1 | ENST00000462594.1 | n.199+246A>G | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.102 AC: 15152AN: 148724Hom.: 934 Cov.: 25 show subpopulations
GnomAD3 genomes
AF:
AC:
15152
AN:
148724
Hom.:
Cov.:
25
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.102 AC: 15168AN: 148780Hom.: 937 Cov.: 25 AF XY: 0.104 AC XY: 7560AN XY: 72372 show subpopulations
GnomAD4 genome
AF:
AC:
15168
AN:
148780
Hom.:
Cov.:
25
AF XY:
AC XY:
7560
AN XY:
72372
show subpopulations
African (AFR)
AF:
AC:
6202
AN:
40438
American (AMR)
AF:
AC:
2039
AN:
14996
Ashkenazi Jewish (ASJ)
AF:
AC:
239
AN:
3452
East Asian (EAS)
AF:
AC:
592
AN:
5036
South Asian (SAS)
AF:
AC:
340
AN:
4680
European-Finnish (FIN)
AF:
AC:
1186
AN:
9590
Middle Eastern (MID)
AF:
AC:
24
AN:
276
European-Non Finnish (NFE)
AF:
AC:
4325
AN:
67356
Other (OTH)
AF:
AC:
183
AN:
2046
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
617
1233
1850
2466
3083
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 20, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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