rs389883

Positions:

• chr6-31979683-G-T

Variant summary

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

The NM_004197.2(STK19):​c.473+130G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 1,285,820 control chromosomes in the GnomAD database, including 344,962 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 0.80 (48871 hom., cov: 29)
  • Exomes 𝑓: 0.72 (296091 hom.)
• Consequence: STK19 NM_004197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK19	NM_004197.2	c.473+130G>T		intron_variant		ENST00000685781.1	NP_004188.2
STK19	NM_032454.1	c.815+130G>T		intron_variant			NP_115830.1
STK19	NR_026717.1	n.1116+130G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK19	ENST00000685781.1	c.473+130G>T		intron_variant			NM_004197.2	ENSP00000509445	P4

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120793 AN: 151920 Hom.: 48804 Cov.: 29

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.833

GnomAD4 exome AF: 0.717 AC: 813373 AN: 1133782 Hom.: 296091 Cov.: 14 AF XY: 0.723 AC XY: 406094 AN XY: 561734

Gnomad4 AFR exome AF: 0.926

Gnomad4 AMR exome AF: 0.847

Gnomad4 ASJ exome AF: 0.866

Gnomad4 EAS exome AF: 0.690

Gnomad4 SAS exome AF: 0.894

Gnomad4 FIN exome AF: 0.725

Gnomad4 NFE exome AF: 0.690

Gnomad4 OTH exome AF: 0.740

GnomAD4 genome AF: 0.795 AC: 120920 AN: 152038 Hom.: 48871 Cov.: 29 AF XY: 0.800 AC XY: 59411 AN XY: 74302

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.834

Alfa AF: 0.739 Hom.: 75195

Bravo AF: 0.808

Asia WGS AF: 0.850 AC: 2958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.76

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: rs389883; hg19: chr6-31947460;