NM_001352389.2:c.-465-1582G>A

Variant names:

• chr11-8482196-C-T
• rs725502
• NM_001352389.2:c.-465-1582G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK33	NM_001352389.2	MANE Select	c.-465-1582G>A		intron	N/A	NP_001339318.1
	STK33	NM_001289061.2		c.-161-7130G>A		intron	N/A	NP_001275990.1
	STK33	NM_001352387.2		c.-195-4913G>A		intron	N/A	NP_001339316.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK33	ENST00000687296.1	MANE Select	c.-465-1582G>A		intron	N/A	ENSP00000509322.1
	STK33	ENST00000315204.5	TSL:1	c.-161-7130G>A		intron	N/A	ENSP00000320754.1
	STK33	ENST00000526517.1	TSL:1	n.178-29290G>A		intron	N/A

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

African (AFR) AF: 0.656 AC: 27214 AN: 41464

American (AMR) AF: 0.527 AC: 8060 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2174 AN: 3466

East Asian (EAS) AF: 0.545 AC: 2812 AN: 5156

South Asian (SAS) AF: 0.644 AC: 3094 AN: 4806

European-Finnish (FIN) AF: 0.460 AC: 4852 AN: 10540

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33761 AN: 67956

Other (OTH) AF: 0.570 AC: 1200 AN: 2106

Alfa AF: 0.522 Hom.: 12001

Bravo AF: 0.554

Asia WGS AF: 0.605 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.44
PhyloP100		-0.31
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: rs725502; hg19: chr11-8503743;