chr13-98457465-CTT-C

Variant names:

• chr13-98457465-CTT-C
• rs11351684
• NM_001032296.4:c.1123-163_1123-162delAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001032296.4(STK24):​c.1123-163_1123-162delAA 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 0.25 (2360 hom., cov: 0)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	NM_001032296.4	MANE Select	c.1123-163_1123-162delAA		intron	N/A	NP_001027467.2
	STK24	NM_003576.5		c.1159-163_1159-162delAA		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.1066-163_1066-162delAA		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.1123-163_1123-162delAA		intron	N/A	ENSP00000442539.2
	STK24	ENST00000376547.7	TSL:1	c.1159-163_1159-162delAA		intron	N/A	ENSP00000365730.3
	STK24	ENST00000444574.1	TSL:1	c.874-163_874-162delAA		intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 27618 AN: 111070 Hom.: 2359 Cov.: 0

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.267

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.249 AC: 27609 AN: 111072 Hom.: 2360 Cov.: 0 AF XY: 0.245 AC XY: 12703 AN XY: 51798

African (AFR) AF: 0.199 AC: 5866 AN: 29408

American (AMR) AF: 0.233 AC: 2495 AN: 10718

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 734 AN: 2926

East Asian (EAS) AF: 0.158 AC: 619 AN: 3924

South Asian (SAS) AF: 0.203 AC: 704 AN: 3476

European-Finnish (FIN) AF: 0.244 AC: 957 AN: 3916

Middle Eastern (MID) AF: 0.266 AC: 59 AN: 222

European-Non Finnish (NFE) AF: 0.287 AC: 15591 AN: 54344

Other (OTH) AF: 0.248 AC: 362 AN: 1458

Alfa AF: 0.102 Hom.: 189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.010
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: rs11351684; hg19: chr13-99109719;