chr10-102140114-A-G
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_015062.5(PPRC1):c.1606A>G(p.Ser536Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,614,220 control chromosomes in the GnomAD database, including 1,296 homozygotes. 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 Benign (no stars).
Frequency
Consequence
NM_015062.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPRC1 | ENST00000278070.7 | c.1606A>G | p.Ser536Gly | missense_variant | Exon 5 of 14 | 1 | NM_015062.5 | ENSP00000278070.2 | ||
PPRC1 | ENST00000413464.6 | c.1606A>G | p.Ser536Gly | missense_variant | Exon 5 of 12 | 2 | ENSP00000399743.2 |
Frequencies
GnomAD3 genomes AF: 0.0180 AC: 2739AN: 152208Hom.: 137 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0351 AC: 8824AN: 251440 AF XY: 0.0331 show subpopulations
GnomAD4 exome AF: 0.0134 AC: 19561AN: 1461894Hom.: 1161 Cov.: 33 AF XY: 0.0143 AC XY: 10402AN XY: 727248 show subpopulations
GnomAD4 genome AF: 0.0180 AC: 2740AN: 152326Hom.: 135 Cov.: 32 AF XY: 0.0207 AC XY: 1543AN XY: 74490 show subpopulations
ClinVar
Submissions by phenotype
PPRC1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at