chr7-94910228-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001166160.2(PPP1R9A):c.115T>A(p.Ser39Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00568 in 1,613,640 control chromosomes in the GnomAD database, including 475 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001166160.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R9A | NM_001166160.2 | c.115T>A | p.Ser39Thr | missense_variant | 2/20 | ENST00000433360.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R9A | ENST00000433360.6 | c.115T>A | p.Ser39Thr | missense_variant | 2/20 | 1 | NM_001166160.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0303 AC: 4594AN: 151704Hom.: 246 Cov.: 32
GnomAD3 exomes AF: 0.00809 AC: 2032AN: 251294Hom.: 97 AF XY: 0.00576 AC XY: 782AN XY: 135826
GnomAD4 exome AF: 0.00312 AC: 4563AN: 1461820Hom.: 227 Cov.: 31 AF XY: 0.00265 AC XY: 1930AN XY: 727198
GnomAD4 genome ? AF: 0.0303 AC: 4602AN: 151820Hom.: 248 Cov.: 32 AF XY: 0.0284 AC XY: 2107AN XY: 74184
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at