9-107487615-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004235.6(KLF4):c.779C>T(p.Pro260Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000437 in 1,600,772 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P260R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004235.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF4 | NM_004235.6 | c.779C>T | p.Pro260Leu | missense_variant | 3/5 | ENST00000374672.5 | |
KLF4 | NM_001314052.2 | c.779C>T | p.Pro260Leu | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF4 | ENST00000374672.5 | c.779C>T | p.Pro260Leu | missense_variant | 3/5 | 1 | NM_004235.6 | P1 | |
KLF4 | ENST00000493306.1 | n.1044C>T | non_coding_transcript_exon_variant | 3/4 | 1 | ||||
KLF4 | ENST00000610832.1 | c.100-425C>T | intron_variant | 5 | |||||
KLF4 | ENST00000497048.5 | n.833C>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151842Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1448930Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 720808
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151842Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74164
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.779C>T (p.P260L) alteration is located in exon 3 (coding exon 3) of the KLF4 gene. This alteration results from a C to T substitution at nucleotide position 779, causing the proline (P) at amino acid position 260 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