chr1-88805953-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_006256.4(PKN2):c.1739G>A(p.Arg580Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,461,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006256.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKN2 | NM_006256.4 | c.1739G>A | p.Arg580Gln | missense_variant | 12/22 | ENST00000370521.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKN2 | ENST00000370521.8 | c.1739G>A | p.Arg580Gln | missense_variant | 12/22 | 1 | NM_006256.4 | P1 | |
PKN2 | ENST00000370513.9 | c.1595G>A | p.Arg532Gln | missense_variant | 11/21 | 1 | |||
PKN2 | ENST00000316005.11 | c.*143G>A | 3_prime_UTR_variant | 11/11 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249208Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135200
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461156Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726930
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2023 | The c.1739G>A (p.R580Q) alteration is located in exon 12 (coding exon 12) of the PKN2 gene. This alteration results from a G to A substitution at nucleotide position 1739, causing the arginine (R) at amino acid position 580 to be replaced by a glutamine (Q). 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