rs149324907
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_052959.3(PANX3):c.493C>T(p.Arg165Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000546 in 1,614,224 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00074 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00053 ( 10 hom. )
Consequence
PANX3
NM_052959.3 missense
NM_052959.3 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 2.05
Publications
6 publications found
Genes affected
PANX3 (HGNC:20573): (pannexin 3) The protein encoded by this gene belongs to the innexin family. Innexin family members are known to be the structural components of gap junctions. [provided by RefSeq, Jul 2008]
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 (MetaRNN=0.0067946017).
BP6
Variant 11-124617442-C-T is Benign according to our data. Variant chr11-124617442-C-T is described in ClinVar as [Benign]. Clinvar id is 1235281.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000742 (113/152368) while in subpopulation EAS AF = 0.0193 (100/5188). AF 95% confidence interval is 0.0162. There are 1 homozygotes in GnomAd4. There are 57 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
BS2
High Homozygotes in GnomAdExome4 at 10 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000742 AC: 113AN: 152250Hom.: 1 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
113
AN:
152250
Hom.:
Cov.:
33
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:
GnomAD2 exomes AF: 0.00134 AC: 336AN: 251462 AF XY: 0.00128 show subpopulations
GnomAD2 exomes
AF:
AC:
336
AN:
251462
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000525 AC: 768AN: 1461856Hom.: 10 Cov.: 32 AF XY: 0.000518 AC XY: 377AN XY: 727226 show subpopulations
GnomAD4 exome
AF:
AC:
768
AN:
1461856
Hom.:
Cov.:
32
AF XY:
AC XY:
377
AN XY:
727226
show subpopulations
African (AFR)
AF:
AC:
2
AN:
33480
American (AMR)
AF:
AC:
1
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
694
AN:
39698
South Asian (SAS)
AF:
AC:
17
AN:
86258
European-Finnish (FIN)
AF:
AC:
1
AN:
53386
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
11
AN:
1112010
Other (OTH)
AF:
AC:
42
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
48
96
145
193
241
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.000742 AC: 113AN: 152368Hom.: 1 Cov.: 33 AF XY: 0.000765 AC XY: 57AN XY: 74512 show subpopulations
GnomAD4 genome
AF:
AC:
113
AN:
152368
Hom.:
Cov.:
33
AF XY:
AC XY:
57
AN XY:
74512
show subpopulations
African (AFR)
AF:
AC:
4
AN:
41590
American (AMR)
AF:
AC:
3
AN:
15312
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
100
AN:
5188
South Asian (SAS)
AF:
AC:
2
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10620
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
2
AN:
68032
Other (OTH)
AF:
AC:
2
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
7
14
21
28
35
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
AF:
AC:
154
Asia WGS
AF:
AC:
15
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 03, 2015
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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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