13-98482066-CAAAA-CAAAAAA

Variant names:

• chr13-98482066-C-CAA
• rs34520150
• NM_001032296.4:c.330+197_330+198dupTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001032296.4(STK24):​c.330+197_330+198dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 99,978 control chromosomes in the GnomAD database, including 17 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.012 (17 hom., cov: 31)
• 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: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0124 (1241/99978) while in subpopulation AFR AF = 0.0411 (1118/27234). AF 95% confidence interval is 0.0391. There are 17 homozygotes in GnomAd4. There are 597 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4	c.330+197_330+198dupTT		intron_variant	Intron 3 of 10	ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.366+197_366+198dupTT		intron_variant	Intron 3 of 10		NP_003567.2
STK24	NM_001286649.2	c.274-6710_274-6709dupTT		intron_variant	Intron 2 of 9		NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.330+198_330+199insTT		intron_variant	Intron 3 of 10	1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1235 AN: 99948 Hom.: 16 Cov.: 31

Gnomad AFR AF: 0.0409

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00928

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00146

Gnomad SAS AF: 0.000327

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000231

Gnomad OTH AF: 0.0135

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

GnomAD4 genome AF: 0.0124 AC: 1241 AN: 99978 Hom.: 17 Cov.: 31 AF XY: 0.0128 AC XY: 597 AN XY: 46794

African (AFR) AF: 0.0411 AC: 1118 AN: 27234

American (AMR) AF: 0.00928 AC: 88 AN: 9486

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2584

East Asian (EAS) AF: 0.00147 AC: 5 AN: 3408

South Asian (SAS) AF: 0.000329 AC: 1 AN: 3036

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 144

European-Non Finnish (NFE) AF: 0.000231 AC: 11 AN: 47606

Other (OTH) AF: 0.0135 AC: 18 AN: 1336

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34520150; hg19: chr13-99134320;