rs2748724

Variant names:

• chrX-132026679-A-C
• rs2748724
• NM_016542.4:c.42+3020A>C

Variant summary

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

The NM_016542.4(STK26):​c.42+3020A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 111,261 control chromosomes in the GnomAD database, including 6,201 homozygotes. There are 12,961 hemizygotes in GnomAD. 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 0.39 (6201 hom., 12961 hem., cov: 23)
• Consequence: STK26 NM_016542.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 2 publications found

Genes affected

STK26 (HGNC:18174): (serine/threonine kinase 26) The product of this gene is a member of the GCK group III family of kinases, which are a subset of the Ste20-like kinases. The encoded protein contains an amino-terminal kinase domain, and a carboxy-terminal regulatory domain that mediates homodimerization. The protein kinase localizes to the Golgi apparatus and is specifically activated by binding to the Golgi matrix protein GM130. It is also cleaved by caspase-3 in vitro, and may function in the apoptotic pathway. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK26	NM_016542.4	c.42+3020A>C		intron_variant	Intron 2 of 11	ENST00000394334.7	NP_057626.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK26	ENST00000394334.7	c.42+3020A>C		intron_variant	Intron 2 of 11	1	NM_016542.4	ENSP00000377867.2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 43678 AN: 111206 Hom.: 6204 Cov.: 23

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.460

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.393 AC: 43683 AN: 111261 Hom.: 6201 Cov.: 23 AF XY: 0.387 AC XY: 12961 AN XY: 33515

African (AFR) AF: 0.327 AC: 10027 AN: 30680

American (AMR) AF: 0.318 AC: 3357 AN: 10565

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1311 AN: 2636

East Asian (EAS) AF: 0.438 AC: 1540 AN: 3513

South Asian (SAS) AF: 0.371 AC: 1002 AN: 2698

European-Finnish (FIN) AF: 0.484 AC: 2852 AN: 5891

Middle Eastern (MID) AF: 0.459 AC: 100 AN: 218

European-Non Finnish (NFE) AF: 0.430 AC: 22720 AN: 52878

Other (OTH) AF: 0.360 AC: 545 AN: 1512

Alfa AF: 0.405 Hom.: 23261

Bravo AF: 0.377

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.70
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: rs2748724; hg19: chrX-131160707;