1-43390239-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001365999.1(SZT2):c.27+244C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,164 control chromosomes in the GnomAD database, including 8,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.33 ( 8508 hom., cov: 33)
Consequence
SZT2
NM_001365999.1 intron
NM_001365999.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0230
Publications
12 publications found
Genes affected
SZT2 (HGNC:29040): (SZT2 subunit of KICSTOR complex) The protein encoded by this gene is expressed in the brain, predominantly in the parietal and frontal cortex as well as in dorsal root ganglia. It is localized to the peroxisome, and is implicated in resistance to oxidative stress. It likely functions by increasing superoxide dismutase (SOD) activity, but itself has no direct SOD activity. Studies in mice show that this gene confers low seizure threshold, and may also enhance epileptogenesis. [provided by RefSeq, Jun 2011]
SZT2 Gene-Disease associations (from GenCC):
- developmental and epileptic encephalopathy, 18Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Illumina
- genetic developmental and epileptic encephalopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- undetermined early-onset epileptic encephalopathyInheritance: 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=-0.9).
BP6
Variant 1-43390239-C-T is Benign according to our data. Variant chr1-43390239-C-T is described in ClinVar as [Benign]. Clinvar id is 1295756.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.328 AC: 49815AN: 152046Hom.: 8503 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
49815
AN:
152046
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.328 AC: 49852AN: 152164Hom.: 8508 Cov.: 33 AF XY: 0.323 AC XY: 24011AN XY: 74390 show subpopulations
GnomAD4 genome
AF:
AC:
49852
AN:
152164
Hom.:
Cov.:
33
AF XY:
AC XY:
24011
AN XY:
74390
show subpopulations
African (AFR)
AF:
AC:
11246
AN:
41522
American (AMR)
AF:
AC:
5693
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
1409
AN:
3468
East Asian (EAS)
AF:
AC:
519
AN:
5192
South Asian (SAS)
AF:
AC:
719
AN:
4828
European-Finnish (FIN)
AF:
AC:
3512
AN:
10568
Middle Eastern (MID)
AF:
AC:
123
AN:
294
European-Non Finnish (NFE)
AF:
AC:
25479
AN:
67982
Other (OTH)
AF:
AC:
799
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1770
3541
5311
7082
8852
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
509
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 15, 2018
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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