rs201139850
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_006031.6(PCNT):c.4139C>T(p.Ala1380Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,574,726 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1380T) has been classified as Uncertain significance.
Frequency
Consequence
NM_006031.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.4139C>T | p.Ala1380Val | missense_variant | 21/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.3785C>T | p.Ala1262Val | missense_variant | 21/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.4139C>T | p.Ala1380Val | missense_variant | 21/47 | 1 | NM_006031.6 | P2 | |
PCNT | ENST00000480896.5 | c.3785C>T | p.Ala1262Val | missense_variant | 21/47 | 1 | A2 | ||
PCNT | ENST00000695558.1 | c.4139C>T | p.Ala1380Val | missense_variant | 21/48 | A2 | |||
PCNT | ENST00000703224.1 | c.*3382C>T | 3_prime_UTR_variant, NMD_transcript_variant | 23/49 |
Frequencies
GnomAD3 genomes AF: 0.000789 AC: 120AN: 152146Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000228 AC: 41AN: 180152Hom.: 1 AF XY: 0.000197 AC XY: 19AN XY: 96640
GnomAD4 exome AF: 0.0000794 AC: 113AN: 1422462Hom.: 1 Cov.: 32 AF XY: 0.0000654 AC XY: 46AN XY: 703806
GnomAD4 genome AF: 0.000782 AC: 119AN: 152264Hom.: 2 Cov.: 33 AF XY: 0.000766 AC XY: 57AN XY: 74456
ClinVar
Submissions by phenotype
Microcephalic osteodysplastic primordial dwarfism type II Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 18, 2014 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 20, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
PCNT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 29, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at