rs389884

chr6-31973120-A-G

Variant summary

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

The NM_004197.2(STK19):c.237+363A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 487,050 control chromosomes in the GnomAD database, including 1,926 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 0.069 (497 hom., cov: 32)
  • Exomes 𝑓: 0.070 (1429 hom.)
• Consequence: STK19 NM_004197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23

Genes affected

STK19 (HGNC:11398): (serine/threonine kinase 19) This gene encodes a serine/threonine kinase which localizes predominantly to the nucleus. Its specific function is unknown; it is possible that phosphorylation of this protein is involved in transcriptional regulation. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6 and expresses two transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK19	NM_004197.2	c.237+363A>G		intron_variant		ENST00000685781.1
STK19	NM_032454.1	c.567+363A>G		intron_variant
STK19	NR_026717.1	n.880+363A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK19	ENST00000685781.1	c.237+363A>G		intron_variant			NM_004197.2	P4

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10509 AN: 152110 Hom.: 497 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0321

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0522

GnomAD4 exome AF: 0.0704 AC: 23582 AN: 334822 Hom.: 1429 Cov.: 0 AF XY: 0.0653 AC XY: 11801 AN XY: 180814

Gnomad4 AFR exome AF: 0.0401

Gnomad4 AMR exome AF: 0.0241

Gnomad4 ASJ exome AF: 0.0404

Gnomad4 EAS exome AF: 0.000116

Gnomad4 SAS exome AF: 0.000160

Gnomad4 FIN exome AF: 0.0906

Gnomad4 NFE exome AF: 0.104

Gnomad4 OTH exome AF: 0.0737

GnomAD4 genome AF: 0.0690 AC: 10506 AN: 152228 Hom.: 497 Cov.: 32 AF XY: 0.0642 AC XY: 4780 AN XY: 74428

Gnomad4 AFR AF: 0.0394

Gnomad4 AMR AF: 0.0320

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0788

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0960 Hom.: 1427

Bravo AF: 0.0646

Asia WGS AF: 0.00520 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	3.7
Dann	Benign	0.88

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: rs389884; hg19: chr6-31940897;