rs2039531
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001365999.1(SZT2):c.6034+11A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,612,742 control chromosomes in the GnomAD database, including 121,820 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.31 ( 8608 hom., cov: 33)
Exomes 𝑓: 0.38 ( 113212 hom. )
Consequence
SZT2
NM_001365999.1 intron
NM_001365999.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.166
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 1-43435340-A-C is Benign according to our data. Variant chr1-43435340-A-C is described in ClinVar as [Benign]. Clinvar id is 260619.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SZT2 | NM_001365999.1 | c.6034+11A>C | intron_variant | ENST00000634258.3 | |||
SZT2 | NM_015284.4 | c.5863+11A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.6034+11A>C | intron_variant | 5 | NM_001365999.1 | P1 | |||
SZT2 | ENST00000562955.2 | c.5863+11A>C | intron_variant | 5 | |||||
SZT2 | ENST00000648058.1 | n.2488+11A>C | intron_variant, non_coding_transcript_variant | ||||||
SZT2 | ENST00000649403.1 | n.784+11A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.312 AC: 47397AN: 151930Hom.: 8610 Cov.: 33
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GnomAD3 exomes AF: 0.325 AC: 81260AN: 249812Hom.: 15248 AF XY: 0.325 AC XY: 43846AN XY: 135008
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GnomAD4 exome AF: 0.383 AC: 558898AN: 1460694Hom.: 113212 Cov.: 36 AF XY: 0.377 AC XY: 273944AN XY: 726630
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GnomAD4 genome ? AF: 0.312 AC: 47415AN: 152048Hom.: 8608 Cov.: 33 AF XY: 0.308 AC XY: 22878AN XY: 74290
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Developmental and epileptic encephalopathy, 18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at