rs725502

Positions:

• chr11-8482196-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352389.2(STK33):​c.-465-1582G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,984 control chromosomes in the GnomAD database, including 23,411 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 0.55 (23411 hom., cov: 32)
• Consequence: STK33 NM_001352389.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

STK33 (HGNC:14568): (serine/threonine kinase 33) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in mitotic DNA damage checkpoint signaling and protein autophosphorylation. Predicted to be located in perinuclear region of cytoplasm. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK33	NM_001352389.2	c.-465-1582G>A		intron_variant		ENST00000687296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK33	ENST00000687296.1	c.-465-1582G>A		intron_variant			NM_001352389.2	P1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83586 AN: 151866 Hom.: 23383 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.550 AC: 83659 AN: 151984 Hom.: 23411 Cov.: 32 AF XY: 0.550 AC XY: 40880 AN XY: 74290

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.570

Alfa AF: 0.523 Hom.: 10820

Bravo AF: 0.554

Asia WGS AF: 0.605 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.44

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: rs725502; hg19: chr11-8503743;