1-2111641-T-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002744.6(PRKCZ):c.335-23621T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,132 control chromosomes in the GnomAD database, including 5,310 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 0.26 ( 5305 hom., cov: 32)
Exomes 𝑓: 0.22 ( 5 hom. )
Consequence
PRKCZ
NM_002744.6 intron
NM_002744.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.81
Publications
10 publications found
Genes affected
PRKCZ (HGNC:9412): (protein kinase C zeta) Protein kinase C (PKC) zeta is a member of the PKC family of serine/threonine kinases which are involved in a variety of cellular processes such as proliferation, differentiation and secretion. Unlike the classical PKC isoenzymes which are calcium-dependent, PKC zeta exhibits a kinase activity which is independent of calcium and diacylglycerol but not of phosphatidylserine. Furthermore, it is insensitive to typical PKC inhibitors and cannot be activated by phorbol ester. Unlike the classical PKC isoenzymes, it has only a single zinc finger module. These structural and biochemical properties indicate that the zeta subspecies is related to, but distinct from other isoenzymes of PKC. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.259 AC: 39412AN: 151898Hom.: 5294 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
39412
AN:
151898
Hom.:
Cov.:
32
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:
GnomAD4 exome AF: 0.216 AC: 25AN: 116Hom.: 5 Cov.: 0 AF XY: 0.239 AC XY: 21AN XY: 88 show subpopulations
GnomAD4 exome
AF:
AC:
25
AN:
116
Hom.:
Cov.:
0
AF XY:
AC XY:
21
AN XY:
88
show subpopulations
African (AFR)
AF:
AC:
2
AN:
6
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
4
South Asian (SAS)
AF:
AC:
0
AN:
6
European-Finnish (FIN)
AF:
AC:
1
AN:
6
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
18
AN:
82
Other (OTH)
AF:
AC:
4
AN:
12
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.535
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.259 AC: 39445AN: 152016Hom.: 5305 Cov.: 32 AF XY: 0.263 AC XY: 19545AN XY: 74310 show subpopulations
GnomAD4 genome
AF:
AC:
39445
AN:
152016
Hom.:
Cov.:
32
AF XY:
AC XY:
19545
AN XY:
74310
show subpopulations
African (AFR)
AF:
AC:
8856
AN:
41488
American (AMR)
AF:
AC:
5180
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
1075
AN:
3464
East Asian (EAS)
AF:
AC:
1285
AN:
5156
South Asian (SAS)
AF:
AC:
1324
AN:
4808
European-Finnish (FIN)
AF:
AC:
3168
AN:
10586
Middle Eastern (MID)
AF:
AC:
44
AN:
294
European-Non Finnish (NFE)
AF:
AC:
17703
AN:
67920
Other (OTH)
AF:
AC:
563
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1486
2972
4459
5945
7431
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
410
820
1230
1640
2050
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
768
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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