chr13-100089129-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000282.4(PCCA):c.9G>C(p.Gly3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,509,222 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. G3G) has been classified as Likely benign.
Frequency
Consequence
NM_000282.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCCA | NM_000282.4 | c.9G>C | p.Gly3= | synonymous_variant | 1/24 | ENST00000376285.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCCA | ENST00000376285.6 | c.9G>C | p.Gly3= | synonymous_variant | 1/24 | 1 | NM_000282.4 | P1 | |
PCCA | ENST00000376286.8 | c.9G>C | p.Gly3= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000376279.7 | c.9G>C | p.Gly3= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000647303.1 | c.9G>C | p.Gly3= | synonymous_variant, NMD_transcript_variant | 1/21 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000219 AC: 3AN: 137272Hom.: 0 AF XY: 0.0000269 AC XY: 2AN XY: 74456
GnomAD4 exome AF: 0.0000103 AC: 14AN: 1356872Hom.: 0 Cov.: 31 AF XY: 0.0000120 AC XY: 8AN XY: 666244
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74500
ClinVar
Submissions by phenotype
Propionic acidemia Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Mar 18, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at