chr13-100089138-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000282.4(PCCA):c.18C>T(p.Val6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000737 in 1,356,526 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. V6V) has been classified as Likely benign.
Frequency
Consequence
NM_000282.4 synonymous
Scores
Clinical Significance
Conservation
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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.18C>T | p.Val6= | synonymous_variant | 1/24 | ENST00000376285.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCCA | ENST00000376285.6 | c.18C>T | p.Val6= | synonymous_variant | 1/24 | 1 | NM_000282.4 | P1 | |
PCCA | ENST00000376286.8 | c.18C>T | p.Val6= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000376279.7 | c.18C>T | p.Val6= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000647303.1 | c.18C>T | p.Val6= | synonymous_variant, NMD_transcript_variant | 1/21 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000760 AC: 1AN: 131512Hom.: 0 AF XY: 0.0000140 AC XY: 1AN XY: 71520
GnomAD4 exome AF: 7.37e-7 AC: 1AN: 1356526Hom.: 0 Cov.: 31 AF XY: 0.00000150 AC XY: 1AN XY: 666556
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Propionic acidemia Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Aug 17, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at