chr13-98482066-CA-C

Variant names:

• chr13-98482066-CA-C
• rs34520150
• NM_001032296.4:c.330+198delT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001032296.4(STK24):​c.330+198delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0062 (0 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• 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: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032296.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	NM_001032296.4	MANE Select	c.330+198delT		intron	N/A	NP_001027467.2	Q9Y6E0-2
	STK24	NM_003576.5		c.366+198delT		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.274-6709delT		intron	N/A	NP_001273578.1	B4DR80

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	ENST00000539966.6	TSL:1 MANE Select	c.330+198delT		intron	N/A	ENSP00000442539.2	Q9Y6E0-2
	STK24	ENST00000376547.7	TSL:1	c.366+198delT		intron	N/A	ENSP00000365730.3	Q9Y6E0-1
	STK24	ENST00000444574.1	TSL:1	c.81+198delT		intron	N/A	ENSP00000402764.1	H0Y630

Frequencies

GnomAD3 genomes AF: 0.00611 AC: 610 AN: 99774 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00460

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00593

Gnomad ASJ AF: 0.00311

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.00164

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.00625

Gnomad NFE AF: 0.00495

Gnomad OTH AF: 0.00606

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00615 AC: 614 AN: 99802 Hom.: 0 Cov.: 31 AF XY: 0.00717 AC XY: 335 AN XY: 46694

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00470 AC: 128 AN: 27262

American (AMR) AF: 0.00592 AC: 56 AN: 9456

Ashkenazi Jewish (ASJ) AF: 0.00311 AC: 8 AN: 2576

East Asian (EAS) AF: 0.00734 AC: 25 AN: 3406

South Asian (SAS) AF: 0.00198 AC: 6 AN: 3036

European-Finnish (FIN) AF: 0.0327 AC: 147 AN: 4500

Middle Eastern (MID) AF: 0.00704 AC: 1 AN: 142

European-Non Finnish (NFE) AF: 0.00495 AC: 235 AN: 47510

Other (OTH) AF: 0.00603 AC: 8 AN: 1326

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000192 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism

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: rs34520150; hg19: chr13-99134320; COSMIC: COSV104427717;