12-27246848-A-G

Variant names:

• chr12-27246848-A-G
• rs10842885
• NM_015000.4:c.-12+2516A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015000.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK38L	NM_015000.4	MANE Select	c.-12+2516A>G		intron	N/A	NP_055815.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK38L	ENST00000389032.8	TSL:1 MANE Select	c.-12+2516A>G		intron	N/A	ENSP00000373684.3
	STK38L	ENST00000545470.5	TSL:3	c.-12+2516A>G		intron	N/A	ENSP00000439457.1
	STK38L	ENST00000541191.5	TSL:4	c.-12+2740A>G		intron	N/A	ENSP00000437856.1

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

African (AFR) AF: 0.623 AC: 25793 AN: 41432

American (AMR) AF: 0.629 AC: 9606 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1917 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4485 AN: 5164

South Asian (SAS) AF: 0.638 AC: 3068 AN: 4810

European-Finnish (FIN) AF: 0.429 AC: 4534 AN: 10562

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27512 AN: 67970

Other (OTH) AF: 0.518 AC: 1092 AN: 2108

Alfa AF: 0.456 Hom.: 2133

Bravo AF: 0.541

Asia WGS AF: 0.729 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.59
PhyloP100		0.097
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10842885; hg19: chr12-27399781;