19-14441432-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002741.5(PKN1):c.311C>T(p.Ala104Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000051 in 1,469,422 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002741.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152102Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000501 AC: 66AN: 1317320Hom.: 1 Cov.: 32 AF XY: 0.0000510 AC XY: 33AN XY: 646426
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.329C>T (p.A110V) alteration is located in exon 2 (coding exon 2) of the PKN1 gene. This alteration results from a C to T substitution at nucleotide position 329, causing the alanine (A) at amino acid position 110 to be replaced by a valine (V). 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