rs2279515

Positions:

• chr5-172126829-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000176763.10(STK10):​c.370+544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,030 control chromosomes in the GnomAD database, including 7,770 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 0.30 (7770 hom., cov: 31)
• Consequence: STK10 ENST00000176763.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

Genes affected

STK10 (HGNC:11388): (serine/threonine kinase 10) This gene encodes a member of the Ste20 family of serine/threonine protein kinases, and is similar to several known polo-like kinase kinases. The protein can associate with and phosphorylate polo-like kinase 1, and overexpression of a kinase-dead version of the protein interferes with normal cell cycle progression. The kinase can also negatively regulate interleukin 2 expression in T-cells via the mitogen activated protein kinase kinase 1 pathway. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK10	NM_005990.4	c.370+544A>G		intron_variant		ENST00000176763.10	NP_005981.3
STK10	XM_047417628.1	c.370+544A>G		intron_variant			XP_047273584.1
STK10	XM_047417629.1	c.370+544A>G		intron_variant			XP_047273585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK10	ENST00000176763.10	c.370+544A>G		intron_variant		1	NM_005990.4	ENSP00000176763	P1
STK10	ENST00000519710.1	n.151+544A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45500 AN: 151912 Hom.: 7743 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.300 AC: 45580 AN: 152030 Hom.: 7770 Cov.: 31 AF XY: 0.297 AC XY: 22051 AN XY: 74322

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.259

Alfa AF: 0.250 Hom.: 4992

Bravo AF: 0.309

Asia WGS AF: 0.197 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.40

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: rs2279515; hg19: chr5-171553833;