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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1R17 | NM_006658.5 | c.438C>A | p.Asp146Glu | missense_variant | Exon 5 of 5 | ENST00000342032.8 | NP_006649.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1R17 | ENST00000342032.8 | c.438C>A | p.Asp146Glu | missense_variant | Exon 5 of 5 | 1 | NM_006658.5 | ENSP00000340125.3 | ||
PPP1R17 | ENST00000409146.3 | c.285C>A | p.Asp95Glu | missense_variant | Exon 4 of 4 | 2 | ENSP00000386459.3 | |||
PPP1R17 | ENST00000498609.1 | n.319C>A | non_coding_transcript_exon_variant | Exon 3 of 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
Submissions by phenotype
not specified Uncertain:1
The c.438C>A (p.D146E) alteration is located in exon 5 (coding exon 4) of the PPP1R17 gene. This alteration results from a C to A substitution at nucleotide position 438, causing the aspartic acid (D) at amino acid position 146 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at