21-46385930-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006031.6(PCNT):c.3411C>T(p.Gly1137=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000427 in 1,614,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G1137G) has been classified as Likely benign.
Frequency
Consequence
NM_006031.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.3411C>T | p.Gly1137= | synonymous_variant | 17/47 | ENST00000359568.10 | |
PCNT | NM_001315529.2 | c.3057C>T | p.Gly1019= | synonymous_variant | 17/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.3411C>T | p.Gly1137= | synonymous_variant | 17/47 | 1 | NM_006031.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251480Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135916
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.0000481 AC XY: 35AN XY: 727234
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74468
ClinVar
Submissions by phenotype
PCNT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 24, 2019 | 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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at