rs4929949

Variant names:

• chr11-8583046-T-C
• rs4929949
• NM_001352389.2:c.-466+11037A>G

Variant summary

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

The NM_001352389.2(STK33):​c.-466+11037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,134 control chromosomes in the GnomAD database, including 16,473 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 0.46 (16473 hom., cov: 32)
• Consequence: STK33 NM_001352389.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.02
• Publications: 131 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]

STK33 Gene-Disease associations (from GenCC):

• spermatogenic failure 93

  Inheritance: AR Classification: LIMITED Submitted by: PanelApp Australia

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352389.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK33	NM_001352389.2	MANE Select	c.-466+11037A>G		intron	N/A	NP_001339318.1	Q9BYT3-1
	STK33	NM_001289061.2		c.-162+10698A>G		intron	N/A	NP_001275990.1	Q9BYT3-1
	STK33	NM_001352387.2		c.-196+11037A>G		intron	N/A	NP_001339316.1	Q9BYT3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK33	ENST00000687296.1	MANE Select	c.-466+11037A>G		intron	N/A	ENSP00000509322.1	Q9BYT3-1
	STK33	ENST00000315204.5	TSL:1	c.-311+10698A>G		intron	N/A	ENSP00000320754.1	Q9BYT3-1
	STK33	ENST00000526517.1	TSL:1	n.177+11037A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70369 AN: 152016 Hom.: 16461 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.463 AC: 70408 AN: 152134 Hom.: 16473 Cov.: 32 AF XY: 0.462 AC XY: 34338 AN XY: 74366

African (AFR) AF: 0.394 AC: 16372 AN: 41506

American (AMR) AF: 0.480 AC: 7333 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2236 AN: 5184

South Asian (SAS) AF: 0.350 AC: 1692 AN: 4830

European-Finnish (FIN) AF: 0.540 AC: 5698 AN: 10558

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34167 AN: 67986

Other (OTH) AF: 0.439 AC: 928 AN: 2112

Alfa AF: 0.485 Hom.: 51986

Bravo AF: 0.462

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.069
DANN	Benign	0.71
PhyloP100		-4.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4929949; hg19: chr11-8604593;