13-98482585-G-C

Variant names:

• chr13-98482585-G-C
• rs2274056
• NM_001032296.4:c.274-264C>G

Variant summary

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

The NM_003576.5(STK24):​c.310-264C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,096 control chromosomes in the GnomAD database, including 22,576 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 0.54 (22576 hom., cov: 32)
• Consequence: STK24 NM_003576.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 1 publications found

Genes affected

STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003576.5. 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
	STK24	NM_001032296.4	MANE Select	c.274-264C>G		intron	N/A	NP_001027467.2
	STK24	NM_003576.5		c.310-264C>G		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.274-7227C>G		intron	N/A	NP_001273578.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	ENST00000539966.6	TSL:1 MANE Select	c.274-264C>G		intron	N/A	ENSP00000442539.2
	STK24	ENST00000376547.7	TSL:1	c.310-264C>G		intron	N/A	ENSP00000365730.3
	STK24	ENST00000444574.1	TSL:1	c.25-264C>G		intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82279 AN: 151978 Hom.: 22554 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.541 AC: 82355 AN: 152096 Hom.: 22576 Cov.: 32 AF XY: 0.533 AC XY: 39634 AN XY: 74362

African (AFR) AF: 0.554 AC: 22965 AN: 41474

American (AMR) AF: 0.498 AC: 7608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1536 AN: 5172

South Asian (SAS) AF: 0.440 AC: 2121 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5252 AN: 10592

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39371 AN: 67966

Other (OTH) AF: 0.532 AC: 1124 AN: 2112

Alfa AF: 0.462 Hom.: 1311

Bravo AF: 0.537

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.38
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: rs2274056; hg19: chr13-99134839;