chr13-98460215-G-GCCTGACA

Position:

• chr13-98460215-G-GCCTGACA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001032296.4(STK24):​c.1122+156_1122+157insTGTCAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 9,548 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0034 (0 hom., cov: 33)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK24	NM_001032296.4	c.1122+156_1122+157insTGTCAGG		intron_variant		ENST00000539966.6
STK24	NM_001286649.2	c.1065+156_1065+157insTGTCAGG		intron_variant
STK24	NM_003576.5	c.1158+156_1158+157insTGTCAGG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK24	ENST00000539966.6	c.1122+156_1122+157insTGTCAGG		intron_variant		1	NM_001032296.4	P1

Frequencies

GnomAD3 genomes AF: 0.00336 AC: 32 AN: 9522 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00281

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0208

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

GnomAD4 genome AF: 0.00335 AC: 32 AN: 9548 Hom.: 0 Cov.: 33 AF XY: 0.00399 AC XY: 19 AN XY: 4762

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00279

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0743

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0208

Bravo AF: 0.0000604

Asia WGS AF: 0.00541 AC: 8 AN: 1480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35458785; hg19: chr13-99112469;