13-73059401-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001730.5(KLF5):c.74C>T(p.Pro25Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000343 in 1,398,324 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
Consequence
NM_001730.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLF5 | ENST00000377687.6 | c.74C>T | p.Pro25Leu | missense_variant | Exon 1 of 4 | 1 | NM_001730.5 | ENSP00000366915.4 | ||
KLF5 | ENST00000539231.5 | c.-12-2460C>T | intron_variant | Intron 1 of 3 | 1 | ENSP00000440407.1 | ||||
KLF5 | ENST00000477333.5 | n.184-2460C>T | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151308Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000249 AC: 1AN: 40110Hom.: 0 AF XY: 0.0000428 AC XY: 1AN XY: 23342
GnomAD4 exome AF: 0.0000361 AC: 45AN: 1247016Hom.: 0 Cov.: 30 AF XY: 0.0000425 AC XY: 26AN XY: 611324
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151308Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73836
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.74C>T (p.P25L) alteration is located in exon 1 (coding exon 1) of the KLF5 gene. This alteration results from a C to T substitution at nucleotide position 74, causing the proline (P) at amino acid position 25 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at