chr5-172126829-T-C

Variant names:

• chr5-172126829-T-C
• rs2279515
• NM_005990.4:c.370+544A>G

Variant summary

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

The NM_005990.4(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 NM_005990.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STK10	NM_005990.4	c.370+544A>G		intron_variant	Intron 3 of 18	ENST00000176763.10	NP_005981.3
STK10	XM_047417628.1	c.370+544A>G		intron_variant	Intron 3 of 17		XP_047273584.1
STK10	XM_047417629.1	c.370+544A>G		intron_variant	Intron 3 of 16		XP_047273585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK10	ENST00000176763.10	c.370+544A>G		intron_variant	Intron 3 of 18	1	NM_005990.4	ENSP00000176763.5
STK10	ENST00000519710.1	n.151+544A>G		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.474 AC: 19630 AN: 41428

American (AMR) AF: 0.241 AC: 3681 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3466

East Asian (EAS) AF: 0.152 AC: 784 AN: 5172

South Asian (SAS) AF: 0.169 AC: 814 AN: 4818

European-Finnish (FIN) AF: 0.262 AC: 2775 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16343 AN: 67974

Other (OTH) AF: 0.259 AC: 545 AN: 2108

Alfa AF: 0.257 Hom.: 7939

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
PhyloP100		0.17
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: rs2279515; hg19: chr5-171553833;