rs387608

chr6-31973780-G-A

Variant summary

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

The NM_004197.2(STK19):c.237+1023G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,010 control chromosomes in the GnomAD database, including 3,579 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 0.19 (3579 hom., cov: 32)
• Consequence: STK19 NM_004197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK19	NM_004197.2	c.237+1023G>A		intron_variant		ENST00000685781.1
STK19	NM_032454.1	c.567+1023G>A		intron_variant
STK19	NR_026717.1	n.880+1023G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK19	ENST00000685781.1	c.237+1023G>A		intron_variant			NM_004197.2	P4

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29120 AN: 151892 Hom.: 3571 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.192 AC: 29162 AN: 152010 Hom.: 3579 Cov.: 32 AF XY: 0.190 AC XY: 14096 AN XY: 74306

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.0670

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.212

Alfa AF: 0.134 Hom.: 2964

Bravo AF: 0.208

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.9
Dann	Benign	0.75

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: rs387608; hg19: chr6-31941557;