rs4929949

Positions:

• chr11-8583046-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK33	NM_001352389.2	c.-466+11037A>G		intron_variant		ENST00000687296.1	NP_001339318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK33	ENST00000687296.1	c.-466+11037A>G		intron_variant			NM_001352389.2	ENSP00000509322	P1

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

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.439

Alfa AF: 0.484 Hom.: 21087

Bravo AF: 0.462

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.069
DANN	Benign	0.71

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: rs4929949; hg19: chr11-8604593;