rs61598773
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000532.5(PCCB):c.546G>A(p.Arg182=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000935 in 1,608,040 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000532.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCCB | NM_000532.5 | c.546G>A | p.Arg182= | splice_region_variant, synonymous_variant | 6/15 | ENST00000251654.9 | |
PCCB | NM_001178014.2 | c.606G>A | p.Arg202= | splice_region_variant, synonymous_variant | 7/16 | ||
PCCB | XM_011512873.2 | c.546G>A | p.Arg182= | splice_region_variant, synonymous_variant | 6/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCCB | ENST00000251654.9 | c.546G>A | p.Arg182= | splice_region_variant, synonymous_variant | 6/15 | 1 | NM_000532.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00494 AC: 751AN: 152160Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00124 AC: 311AN: 251410Hom.: 2 AF XY: 0.000839 AC XY: 114AN XY: 135886
GnomAD4 exome AF: 0.000518 AC: 754AN: 1455762Hom.: 8 Cov.: 29 AF XY: 0.000429 AC XY: 311AN XY: 724820
GnomAD4 genome ? AF: 0.00492 AC: 749AN: 152278Hom.: 4 Cov.: 32 AF XY: 0.00485 AC XY: 361AN XY: 74470
ClinVar
Submissions by phenotype
Propionic acidemia Benign:3
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 22, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 05, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at