2-219246836-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001330213.2(STK16):c.266G>T(p.Gly89Val) variant causes a missense change. The variant allele was found at a frequency of 0.000234 in 1,613,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 0 hom. )
Consequence
STK16
NM_001330213.2 missense
NM_001330213.2 missense
Scores
1
10
7
Clinical Significance
Conservation
PhyloP100: 6.15
Genes affected
STK16 (HGNC:11394): (serine/threonine kinase 16) Predicted to enable protein serine/threonine kinase activity. Involved in protein autophosphorylation. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.27396965).
BS2
?
High AC in GnomAd at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK16 | NM_001330213.2 | c.266G>T | p.Gly89Val | missense_variant | 3/8 | ENST00000396738.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK16 | ENST00000396738.7 | c.266G>T | p.Gly89Val | missense_variant | 3/8 | 2 | NM_001330213.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152194Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000120 AC: 30AN: 249264Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135208
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GnomAD4 exome AF: 0.000242 AC: 353AN: 1461458Hom.: 0 Cov.: 31 AF XY: 0.000234 AC XY: 170AN XY: 726936
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GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74360
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.266G>T (p.G89V) alteration is located in exon 3 (coding exon 2) of the STK16 gene. This alteration results from a G to T substitution at nucleotide position 266, causing the glycine (G) at amino acid position 89 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N;N;D
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Benign
T;T;D;T
Polyphen
D;D;B;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at