rs614028

Positions:

• chr6-36516475-G-A
• chr6-36516475-G-C
• chr6-36516475-G-T

Variant summary

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

The NM_007271.4(STK38):​c.515-983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,084 control chromosomes in the GnomAD database, including 16,478 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 0.44 (16478 hom., cov: 32)
• Consequence: STK38 NM_007271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK38	NM_007271.4	c.515-983C>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.515-983C>T		intron_variant		1	NM_007271.4	ENSP00000229812.7

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66584 AN: 151966 Hom.: 16431 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.439 AC: 66696 AN: 152084 Hom.: 16478 Cov.: 32 AF XY: 0.440 AC XY: 32730 AN XY: 74330

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.427

Alfa AF: 0.369 Hom.: 4478

Bravo AF: 0.464

Asia WGS AF: 0.446 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.94
DANN	Benign	0.49

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: rs614028; hg19: chr6-36484252;