rs41286082
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001730.5(KLF5):c.*340T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 203,258 control chromosomes in the GnomAD database, including 189 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 0.026 ( 179 hom., cov: 33)
Exomes 𝑓: 0.0045 ( 10 hom. )
Consequence
KLF5
NM_001730.5 3_prime_UTR
NM_001730.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.29
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0887 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF5 | NM_001730.5 | c.*340T>C | 3_prime_UTR_variant | 4/4 | ENST00000377687.6 | ||
KLF5 | NM_001286818.2 | c.*340T>C | 3_prime_UTR_variant | 4/4 | |||
KLF5 | XM_047430553.1 | c.*340T>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF5 | ENST00000377687.6 | c.*340T>C | 3_prime_UTR_variant | 4/4 | 1 | NM_001730.5 | P3 | ||
KLF5 | ENST00000539231.5 | c.*340T>C | 3_prime_UTR_variant | 4/4 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0264 AC: 4007AN: 152046Hom.: 179 Cov.: 33
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GnomAD4 exome AF: 0.00452 AC: 231AN: 51094Hom.: 10 Cov.: 0 AF XY: 0.00386 AC XY: 99AN XY: 25646
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GnomAD4 genome ? AF: 0.0263 AC: 4007AN: 152164Hom.: 179 Cov.: 33 AF XY: 0.0253 AC XY: 1881AN XY: 74410
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at