12-9893038-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001190765.1(KLRF2):c.236C>T(p.Pro79Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,535,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001190765.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLRF2 | NM_001190765.1 | c.236C>T | p.Pro79Leu | missense_variant | 4/6 | ENST00000535540.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLRF2 | ENST00000535540.1 | c.236C>T | p.Pro79Leu | missense_variant | 4/6 | 1 | NM_001190765.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000223 AC: 3AN: 134412Hom.: 0 AF XY: 0.0000137 AC XY: 1AN XY: 73212
GnomAD4 exome AF: 0.00000940 AC: 13AN: 1383208Hom.: 0 Cov.: 30 AF XY: 0.00000879 AC XY: 6AN XY: 682558
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.236C>T (p.P79L) alteration is located in exon 4 (coding exon 4) of the KLRF2 gene. This alteration results from a C to T substitution at nucleotide position 236, causing the proline (P) at amino acid position 79 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