11-125410304-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001382323.2(PKNOX2):c.697G>A(p.Val233Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000936 in 1,613,848 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKNOX2 | NM_001382323.2 | c.697G>A | p.Val233Ile | missense_variant | 8/13 | ENST00000298282.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKNOX2 | ENST00000298282.14 | c.697G>A | p.Val233Ile | missense_variant | 8/13 | 1 | NM_001382323.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000642 AC: 16AN: 249384Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135310
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461774Hom.: 1 Cov.: 32 AF XY: 0.0000825 AC XY: 60AN XY: 727194
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.697G>A (p.V233I) alteration is located in exon 8 (coding exon 5) of the PKNOX2 gene. This alteration results from a G to A substitution at nucleotide position 697, causing the valine (V) at amino acid position 233 to be replaced by an isoleucine (I). 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