12-27246848-A-G

Variant summary

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

The NM_015000.4(STK38L):c.-12+2516A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,988 control chromosomes in the GnomAD database, including 21,636 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 0.52 (21636 hom., cov: 32)
• Consequence: STK38L NM_015000.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

Genes affected

STK38L (HGNC:17848): (serine/threonine kinase 38 like) Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in intracellular signal transduction. Acts upstream of or within protein phosphorylation. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK38L	NM_015000.4	c.-12+2516A>G		intron_variant		ENST00000389032.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK38L	ENST00000389032.8	c.-12+2516A>G		intron_variant		1	NM_015000.4	P1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78561 AN: 151870 Hom.: 21595 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.518 AC: 78658 AN: 151988 Hom.: 21636 Cov.: 32 AF XY: 0.526 AC XY: 39043 AN XY: 74270

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.518

Alfa AF: 0.451 Hom.: 1999

Bravo AF: 0.541

Asia WGS AF: 0.729 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.2
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10842885; hg19: chr12-27399781;