rs614028

Variant names:

• chr6-36516475-G-A
• rs614028
• NM_007271.4:c.515-983C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STK38	NM_007271.4	c.515-983C>T		intron_variant	Intron 6 of 13	ENST00000229812.8	NP_009202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK38	ENST00000229812.8	c.515-983C>T		intron_variant	Intron 6 of 13	1	NM_007271.4	ENSP00000229812.7
STK38	ENST00000850860.1	c.515-983C>T		intron_variant	Intron 6 of 13			ENSP00000520947.1

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

African (AFR) AF: 0.651 AC: 27002 AN: 41476

American (AMR) AF: 0.503 AC: 7688 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2834 AN: 5178

South Asian (SAS) AF: 0.370 AC: 1785 AN: 4820

European-Finnish (FIN) AF: 0.387 AC: 4090 AN: 10568

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.308 AC: 20944 AN: 67982

Other (OTH) AF: 0.427 AC: 903 AN: 2114

Alfa AF: 0.373 Hom.: 5501

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
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs614028; hg19: chr6-36484252;