13-73059353-G-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001730.5(KLF5):c.26G>A(p.Ser9Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KLF5
NM_001730.5 missense
NM_001730.5 missense
Scores
2
4
12
Clinical Significance
Conservation
PhyloP100: 0.844
Publications
0 publications found
Genes affected
KLF5 (HGNC:6349): (KLF transcription factor 5) This gene encodes a member of the Kruppel-like factor subfamily of zinc finger proteins. The encoded protein is a transcriptional activator that binds directly to a specific recognition motif in the promoters of target genes. This protein acts downstream of multiple different signaling pathways and is regulated by post-translational modification. It may participate in both promoting and suppressing cell proliferation. Expression of this gene may be changed in a variety of different cancers and in cardiovascular disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16276965).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001730.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KLF5 | TSL:1 MANE Select | c.26G>A | p.Ser9Asn | missense | Exon 1 of 4 | ENSP00000366915.4 | Q13887-1 | ||
| KLF5 | TSL:1 | c.-12-2508G>A | intron | N/A | ENSP00000440407.1 | Q13887-4 | |||
| KLF5 | c.26G>A | p.Ser9Asn | missense | Exon 1 of 3 | ENSP00000521250.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1269170Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 624258
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1269170
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
624258
African (AFR)
AF:
AC:
0
AN:
25822
American (AMR)
AF:
AC:
0
AN:
21268
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21108
East Asian (EAS)
AF:
AC:
0
AN:
27692
South Asian (SAS)
AF:
AC:
0
AN:
65842
European-Finnish (FIN)
AF:
AC:
0
AN:
30958
Middle Eastern (MID)
AF:
AC:
0
AN:
3634
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1021082
Other (OTH)
AF:
AC:
0
AN:
51764
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Loss of phosphorylation at S9 (P = 0.0404)
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
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
Publications
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