rs79308790
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_StrongBA1
The ENST00000454220.7(PPP2R1A):āc.108A>Cā(p.Arg36Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00346 in 1,547,534 control chromosomes in the GnomAD database, including 152 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
ENST00000454220.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R1A | NM_014225.6 | c.78+30A>C | intron_variant | ENST00000322088.11 | |||
PPP2R1A | NR_033500.2 | n.123+30A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R1A | ENST00000322088.11 | c.78+30A>C | intron_variant | 1 | NM_014225.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0184 AC: 2804AN: 152188Hom.: 96 Cov.: 33
GnomAD3 exomes AF: 0.00399 AC: 593AN: 148444Hom.: 17 AF XY: 0.00324 AC XY: 256AN XY: 79026
GnomAD4 exome AF: 0.00183 AC: 2548AN: 1395228Hom.: 56 Cov.: 31 AF XY: 0.00158 AC XY: 1089AN XY: 688216
GnomAD4 genome ? AF: 0.0185 AC: 2812AN: 152306Hom.: 96 Cov.: 33 AF XY: 0.0177 AC XY: 1320AN XY: 74470
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at