11-8338866-C-T

Variant names:

• chr11-8338866-C-T
• rs10769903
• XM_047427469.1:c.1345-3240G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047427469.1(STK33):​c.1345-3240G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,974 control chromosomes in the GnomAD database, including 15,787 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 0.45 (15787 hom., cov: 32)
• Consequence: STK33 XM_047427469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK33	XM_047427469.1	c.1345-3240G>A		intron_variant	Intron 14 of 14		XP_047283425.1
STK33	XR_007062494.1	n.1739-3240G>A		intron_variant	Intron 12 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67790 AN: 151856 Hom.: 15766 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.446 AC: 67846 AN: 151974 Hom.: 15787 Cov.: 32 AF XY: 0.444 AC XY: 32971 AN XY: 74278

African (AFR) AF: 0.349 AC: 14447 AN: 41452

American (AMR) AF: 0.417 AC: 6371 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2171 AN: 5162

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4818

European-Finnish (FIN) AF: 0.576 AC: 6088 AN: 10578

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34448 AN: 67916

Other (OTH) AF: 0.406 AC: 856 AN: 2110

Alfa AF: 0.473 Hom.: 2071

Bravo AF: 0.436

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.076
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10769903; hg19: chr11-8360413;