1-44129504-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173484.4(KLF17):c.233C>T(p.Pro78Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,612,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173484.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLF17 | ENST00000372299.4 | c.233C>T | p.Pro78Leu | missense_variant | Exon 2 of 4 | 1 | NM_173484.4 | ENSP00000361373.3 | ||
KLF17 | ENST00000476802.1 | n.233C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | ENSP00000489364.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249892Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 135004
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460416Hom.: 0 Cov.: 52 AF XY: 0.0000372 AC XY: 27AN XY: 726402
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.233C>T (p.P78L) alteration is located in exon 2 (coding exon 2) of the KLF17 gene. This alteration results from a C to T substitution at nucleotide position 233, causing the proline (P) at amino acid position 78 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