2-196136183-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.497
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 UniProt
STK17BNM_004226.4 linkuse as main transcriptc.*1264C>T 3_prime_UTR_variant 8/8 ENST00000263955.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STK17BENST00000263955.9 linkuse as main transcriptc.*1264C>T 3_prime_UTR_variant 8/81 NM_004226.4 P1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7581626; hg19: chr2-197000907; API