chr7-94910915-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001166160.2(PPP1R9A):c.802A>T(p.Thr268Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,614,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001166160.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1R9A | NM_001166160.2 | c.802A>T | p.Thr268Ser | missense_variant | 2/20 | ENST00000433360.6 | NP_001159632.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1R9A | ENST00000433360.6 | c.802A>T | p.Thr268Ser | missense_variant | 2/20 | 1 | NM_001166160.2 | ENSP00000405514 |
Frequencies
GnomAD3 genomes AF: 0.000920 AC: 140AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000235 AC: 59AN: 250834Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135602
GnomAD4 exome AF: 0.0000869 AC: 127AN: 1461812Hom.: 0 Cov.: 31 AF XY: 0.0000715 AC XY: 52AN XY: 727196
GnomAD4 genome AF: 0.000919 AC: 140AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000913 AC XY: 68AN XY: 74514
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | PPP1R9A: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at