11-125367939-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001382323.2(PKNOX2):c.181A>C(p.Ile61Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,613,270 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001382323.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKNOX2 | NM_001382323.2 | c.181A>C | p.Ile61Leu | missense_variant | 5/13 | ENST00000298282.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKNOX2 | ENST00000298282.14 | c.181A>C | p.Ile61Leu | missense_variant | 5/13 | 1 | NM_001382323.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152046Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000258 AC: 64AN: 248030Hom.: 1 AF XY: 0.000319 AC XY: 43AN XY: 134664
GnomAD4 exome AF: 0.000127 AC: 185AN: 1461104Hom.: 2 Cov.: 31 AF XY: 0.000149 AC XY: 108AN XY: 726844
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.181A>C (p.I61L) alteration is located in exon 5 (coding exon 2) of the PKNOX2 gene. This alteration results from a A to C substitution at nucleotide position 181, causing the isoleucine (I) at amino acid position 61 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