chr5-172132527-G-A

Position:

• chr5-172132527-G-A

Variant summary

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

The NM_005990.4(STK10):​c.322-5106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 152,046 control chromosomes in the GnomAD database, including 627 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 0.076 (627 hom., cov: 31)
• Consequence: STK10 NM_005990.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK10	NM_005990.4	c.322-5106C>T		intron_variant		ENST00000176763.10
STK10	XM_047417628.1	c.322-5106C>T		intron_variant
STK10	XM_047417629.1	c.322-5106C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK10	ENST00000176763.10	c.322-5106C>T		intron_variant		1	NM_005990.4	P1
STK10	ENST00000519710.1	n.103-5106C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11523 AN: 151928 Hom.: 629 Cov.: 31

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.0779

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0758 AC: 11519 AN: 152046 Hom.: 627 Cov.: 31 AF XY: 0.0798 AC XY: 5930 AN XY: 74336

Gnomad4 AFR AF: 0.0156

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.0972

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0849 Hom.: 98

Bravo AF: 0.0653

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.8
DANN	Benign	0.63

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: rs17570583; hg19: chr5-171559531;