2-196136183-G-A

Position:

• chr2-196136183-G-A

Variant summary

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

The NM_004226.4(STK17B):​c.*1264C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,100 control chromosomes in the GnomAD database, including 31,634 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 0.64 (31634 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: STK17B NM_004226.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

STK17B (HGNC:11396): (serine/threonine kinase 17b) Enables ATP binding activity and protein serine/threonine kinase activity. Involved in intracellular signal transduction; positive regulation of fibroblast apoptotic process; and protein phosphorylation. Located in nucleus. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK17B	NM_004226.4	c.*1264C>T		3_prime_UTR_variant	8/8	ENST00000263955.9	NP_004217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK17B	ENST00000263955.9	c.*1264C>T		3_prime_UTR_variant	8/8	1	NM_004226.4	ENSP00000263955	P1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97519 AN: 151982 Hom.: 31604 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.631

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.642 AC: 97597 AN: 152100 Hom.: 31634 Cov.: 32 AF XY: 0.646 AC XY: 48010 AN XY: 74348

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.633

Alfa AF: 0.636 Hom.: 41893

Bravo AF: 0.641

Asia WGS AF: 0.774 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.80
DANN	Benign	0.50

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: rs7581626; hg19: chr2-197000907;