21-46324276-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006031.6(PCNT):c.48G>A(p.Arg16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000354 in 1,610,924 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. R16R) has been classified as Likely benign.
Frequency
Consequence
NM_006031.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCNT | NM_006031.6 | c.48G>A | p.Arg16= | synonymous_variant | 1/47 | ENST00000359568.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNT | ENST00000359568.10 | c.48G>A | p.Arg16= | synonymous_variant | 1/47 | 1 | NM_006031.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.00000828 AC: 2AN: 241674Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131248
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1458660Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 725504
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 35 AF XY: 0.0000403 AC XY: 3AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at