1-43390239-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0230

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]

ACMG classification

Verdict is Benign. Variant got -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

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SZT2	NM_001365999.1	c.27+244C>T		intron_variant		ENST00000634258.3
SZT2	NM_015284.4	c.27+244C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SZT2	ENST00000634258.3	c.27+244C>T		intron_variant		5	NM_001365999.1	P1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49815 AN: 152046 Hom.: 8503 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.381

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.328 AC: 49852 AN: 152164 Hom.: 8508 Cov.: 33 AF XY: 0.323 AC XY: 24011 AN XY: 74390

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.379

Alfa AF: 0.347 Hom.: 1168

Bravo AF: 0.331

Asia WGS AF: 0.146 AC: 509 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.9
Dann	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs839754; hg19: chr1-43855910;