rs119479063
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006031.6(PCNT):c.3109G>A(p.Glu1037Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,692 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_006031.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.3109G>A | p.Glu1037Lys | missense_variant | 15/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.2755G>A | p.Glu919Lys | missense_variant | 15/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.3109G>A | p.Glu1037Lys | missense_variant | 15/47 | 1 | NM_006031.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249674Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135266
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461502Hom.: 0 Cov.: 63 AF XY: 0.0000124 AC XY: 9AN XY: 727040
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
PCNT-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 13, 2024 | The PCNT c.3109G>A variant is predicted to result in the amino acid substitution p.Glu1037Lys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.016% of alleles in individuals of African descent in gnomAD. 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