chr13-98457465-C-CTT

Position:

• chr13-98457465-C-CTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001032296.4(STK24):​c.1123-163_1123-162dupAA 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 0.0084 (12 hom., cov: 0)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK24	NM_001032296.4	c.1123-163_1123-162dupAA		intron_variant		ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.1159-163_1159-162dupAA		intron_variant			NP_003567.2
STK24	NM_001286649.2	c.1066-163_1066-162dupAA		intron_variant			NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.1123-163_1123-162dupAA		intron_variant		1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.00841 AC: 932 AN: 110782 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.00518

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00730

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.000507

Gnomad SAS AF: 0.00516

Gnomad FIN AF: 0.00385

Gnomad MID AF: 0.0167

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.00843 AC: 934 AN: 110784 Hom.: 12 Cov.: 0 AF XY: 0.00806 AC XY: 416 AN XY: 51616

Gnomad4 AFR AF: 0.00517

Gnomad4 AMR AF: 0.00729

Gnomad4 ASJ AF: 0.0280

Gnomad4 EAS AF: 0.000508

Gnomad4 SAS AF: 0.00519

Gnomad4 FIN AF: 0.00385

Gnomad4 NFE AF: 0.0104

Gnomad4 OTH AF: 0.0136

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: rs11351684; hg19: chr13-99109719;