chr1-88805644-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006256.4(PKN2):c.1649G>A(p.Arg550His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,461,764 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_006256.4 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 |
---|---|---|---|---|---|---|---|
PKN2 | NM_006256.4 | c.1649G>A | p.Arg550His | missense_variant | 11/22 | ENST00000370521.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKN2 | ENST00000370521.8 | c.1649G>A | p.Arg550His | missense_variant | 11/22 | 1 | NM_006256.4 | P1 | |
PKN2 | ENST00000370513.9 | c.1505G>A | p.Arg502His | missense_variant | 10/21 | 1 | |||
PKN2 | ENST00000316005.11 | c.1649G>A | p.Arg550His | missense_variant | 11/11 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000442 AC: 11AN: 249116Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135156
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727178
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.1649G>A (p.R550H) alteration is located in exon 11 (coding exon 11) of the PKN2 gene. This alteration results from a G to A substitution at nucleotide position 1649, causing the arginine (R) at amino acid position 550 to be replaced by a histidine (H). 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