rs3730251
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_000944.5(PPP3CA):c.249G>T(p.Ala83Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,344 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A83A) has been classified as Benign.
Frequency
Consequence
NM_000944.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP3CA | NM_000944.5 | c.249G>T | p.Ala83Ala | synonymous_variant | Exon 2 of 14 | ENST00000394854.8 | NP_000935.1 | |
PPP3CA | NM_001130691.2 | c.249G>T | p.Ala83Ala | synonymous_variant | Exon 2 of 13 | NP_001124163.1 | ||
PPP3CA | NM_001130692.2 | c.249G>T | p.Ala83Ala | synonymous_variant | Exon 2 of 12 | NP_001124164.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250614Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135424
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461344Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726952
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy 91;C4748872:Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at