6-122717826-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_181795.3(PKIB):āc.32T>Cā(p.Val11Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000304 in 1,614,030 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 (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.000033 ( 0 hom. )
Consequence
PKIB
NM_181795.3 missense
NM_181795.3 missense
Scores
2
10
6
Clinical Significance
Conservation
PhyloP100: 4.53
Genes affected
PKIB (HGNC:9018): (cAMP-dependent protein kinase inhibitor beta) This gene encodes a member of the cAMP-dependent protein kinase inhibitor family. The encoded protein may play a role in the protein kinase A (PKA) pathway by interacting with the catalytic subunit of PKA, and overexpression of this gene may play a role in prostate cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3688192).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKIB | NM_181795.3 | c.32T>C | p.Val11Ala | missense_variant | 4/5 | ENST00000368452.7 | NP_861460.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKIB | ENST00000368452.7 | c.32T>C | p.Val11Ala | missense_variant | 4/5 | 1 | NM_181795.3 | ENSP00000357437.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000171 AC: 43AN: 250772Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135486
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GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727198
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74354
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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 04, 2024 | The c.32T>C (p.V11A) alteration is located in exon 4 (coding exon 1) of the PKIB gene. This alteration results from a T to C substitution at nucleotide position 32, causing the valine (V) at amino acid position 11 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
.;D;D;D;D;.;D;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;.;.;T;.;.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Uncertain
T
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;D;D;D;D;D;D;D
REVEL
Uncertain
Sift
Pathogenic
.;D;D;D;D;D;D;D
Sift4G
Pathogenic
D;D;D;D;D;D;D;D
Polyphen
1.0
.;D;D;D;D;.;D;.
Vest4
MutPred
0.66
.;Gain of glycosylation at S6 (P = 0.0816);Gain of glycosylation at S6 (P = 0.0816);Gain of glycosylation at S6 (P = 0.0816);Gain of glycosylation at S6 (P = 0.0816);.;Gain of glycosylation at S6 (P = 0.0816);.;
MVP
MPC
0.55
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at