chr13-100089126-G-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.6G>T(p.Ala2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000074 in 1,351,434 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. A2A) 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.6G>T | p.Ala2= | synonymous_variant | 1/24 | ENST00000376285.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCCA | ENST00000376285.6 | c.6G>T | p.Ala2= | synonymous_variant | 1/24 | 1 | NM_000282.4 | P1 | |
PCCA | ENST00000376286.8 | c.6G>T | p.Ala2= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000376279.7 | c.6G>T | p.Ala2= | synonymous_variant | 1/23 | 2 | |||
PCCA | ENST00000647303.1 | c.6G>T | p.Ala2= | synonymous_variant, NMD_transcript_variant | 1/21 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 7.40e-7 AC: 1AN: 1351434Hom.: 0 Cov.: 30 AF XY: 0.00000151 AC XY: 1AN XY: 662924
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Propionic acidemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.