rs387906928
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006031.6(PCNT):c.3460G>A(p.Glu1154Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,946 control chromosomes in the GnomAD database, including 1 homozygotes. 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_006031.6 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 |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.3460G>A | p.Glu1154Lys | missense_variant | 17/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.3106G>A | p.Glu1036Lys | missense_variant | 17/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.3460G>A | p.Glu1154Lys | missense_variant | 17/47 | 1 | NM_006031.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251194Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135802
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461738Hom.: 1 Cov.: 32 AF XY: 0.0000385 AC XY: 28AN XY: 727180
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
PCNT-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 11, 2023 | The PCNT c.3460G>A variant is predicted to result in the amino acid substitution p.Glu1154Lys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.029% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/21-47805894-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at