7-31707253-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006658.5(PPP1R17):c.438C>A(p.Asp146Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006658.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R17 | NM_006658.5 | c.438C>A | p.Asp146Glu | missense_variant | 5/5 | ENST00000342032.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R17 | ENST00000342032.8 | c.438C>A | p.Asp146Glu | missense_variant | 5/5 | 1 | NM_006658.5 | P1 | |
PPP1R17 | ENST00000409146.3 | c.285C>A | p.Asp95Glu | missense_variant | 4/4 | 2 | |||
PPP1R17 | ENST00000498609.1 | n.319C>A | non_coding_transcript_exon_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251208Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135780
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727126
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74304
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at