NM_001352389.2:c.-466+17764G>T

Variant names:

• chr11-8576319-C-A
• rs11041994
• NM_001352389.2:c.-466+17764G>T

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+17764G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,968 control chromosomes in the GnomAD database, including 17,650 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 0.48 (17650 hom., cov: 32)
• Consequence: STK33 NM_001352389.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 9 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK33	NM_001352389.2	c.-466+17764G>T		intron_variant	Intron 1 of 15	ENST00000687296.1	NP_001339318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK33	ENST00000687296.1	c.-466+17764G>T		intron_variant	Intron 1 of 15		NM_001352389.2	ENSP00000509322.1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73016 AN: 151850 Hom.: 17630 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.481 AC: 73082 AN: 151968 Hom.: 17650 Cov.: 32 AF XY: 0.484 AC XY: 35914 AN XY: 74236

African (AFR) AF: 0.461 AC: 19120 AN: 41448

American (AMR) AF: 0.492 AC: 7502 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2672 AN: 5152

South Asian (SAS) AF: 0.639 AC: 3078 AN: 4816

European-Finnish (FIN) AF: 0.437 AC: 4606 AN: 10552

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32364 AN: 67964

Other (OTH) AF: 0.517 AC: 1090 AN: 2108

Alfa AF: 0.480 Hom.: 48818

Bravo AF: 0.477

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.9
DANN	Benign	0.43
PhyloP100		0.46
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: rs11041994; hg19: chr11-8597866;