rs10223126

Variant names:

• chr5-172152597-C-G
• rs10223126
• NM_005990.4:c.321+4027G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-172152597-C-G
• chr5-172152597-C-T

Variant summary

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

The NM_005990.4(STK10):​c.321+4027G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,176 control chromosomes in the GnomAD database, including 1,025 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 0.11 (1025 hom., cov: 33)
• Consequence: STK10 NM_005990.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005990.4. 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
	STK10	NM_005990.4	MANE Select	c.321+4027G>C		intron	N/A	NP_005981.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK10	ENST00000176763.10	TSL:1 MANE Select	c.321+4027G>C		intron	N/A	ENSP00000176763.5
	STK10	ENST00000519710.1	TSL:2	n.102+4027G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16459 AN: 152058 Hom.: 1022 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.108 AC: 16479 AN: 152176 Hom.: 1025 Cov.: 33 AF XY: 0.109 AC XY: 8080 AN XY: 74412

African (AFR) AF: 0.158 AC: 6552 AN: 41498

American (AMR) AF: 0.0836 AC: 1278 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.137 AC: 661 AN: 4826

European-Finnish (FIN) AF: 0.0888 AC: 941 AN: 10596

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6246 AN: 67990

Other (OTH) AF: 0.112 AC: 237 AN: 2116

Alfa AF: 0.0281 Hom.: 24

Bravo AF: 0.107

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.35
PhyloP100		-0.14
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: rs10223126; hg19: chr5-171579601;