rs140366288
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001365999.1(SZT2):c.3309+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,612,260 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 6 hom. )
Consequence
SZT2
NM_001365999.1 intron
NM_001365999.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.34
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 1-43426818-C-T is Benign according to our data. Variant chr1-43426818-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 416959.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-43426818-C-T is described in Lovd as [Likely_benign].
BS2
?
High Homozygotes in GnomAdExome4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SZT2 | NM_001365999.1 | c.3309+9C>T | intron_variant | ENST00000634258.3 | |||
SZT2 | NM_015284.4 | c.3138+9C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.3309+9C>T | intron_variant | 5 | NM_001365999.1 | P1 | |||
SZT2 | ENST00000562955.2 | c.3138+9C>T | intron_variant | 5 | |||||
SZT2 | ENST00000470139.1 | c.*176+9C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00107 AC: 163AN: 152174Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000869 AC: 214AN: 246276Hom.: 0 AF XY: 0.000863 AC XY: 115AN XY: 133242
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GnomAD4 exome AF: 0.00143 AC: 2094AN: 1459968Hom.: 6 Cov.: 31 AF XY: 0.00140 AC XY: 1020AN XY: 726216
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GnomAD4 genome ? AF: 0.00108 AC: 164AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000859 AC XY: 64AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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DANN
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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