rs2300064

Positions:

• chr6-36506364-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007271.4(STK38):​c.834+219C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,950 control chromosomes in the GnomAD database, including 6,772 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6772 hom., cov: 31)
• Consequence: STK38 NM_007271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

Genes affected

STK38 (HGNC:17847): (serine/threonine kinase 38) This gene encodes a member of the AGC serine/threonine kinase family of proteins. The kinase activity of this protein is regulated by autophosphorylation and phosphorylation by other upstream kinases. This protein has been shown to function in the cell cycle and apoptosis. This protein has also been found to regulate the protein stability and transcriptional activity of the MYC oncogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK38	NM_007271.4	c.834+219C>T		intron_variant		ENST00000229812.8	NP_009202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK38	ENST00000229812.8	c.834+219C>T		intron_variant		1	NM_007271.4	ENSP00000229812.7

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42111 AN: 151832 Hom.: 6756 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.278 AC: 42175 AN: 151950 Hom.: 6772 Cov.: 31 AF XY: 0.278 AC XY: 20610 AN XY: 74266

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.275

Alfa AF: 0.214 Hom.: 1787

Bravo AF: 0.289

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.42

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

Publications

LitVar

Other links and lift over

dbSNP: rs2300064; hg19: chr6-36474141;