chr1-204409526-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032833.5(PPP1R15B):āc.1886C>Gā(p.Ser629Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000826 in 1,613,160 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_032833.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R15B | NM_032833.5 | c.1886C>G | p.Ser629Cys | missense_variant | 1/2 | ENST00000367188.5 | |
PPP1R15B | XM_005245551.6 | c.1886C>G | p.Ser629Cys | missense_variant | 1/3 | ||
PPP1R15B | XM_047432518.1 | c.1886C>G | p.Ser629Cys | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R15B | ENST00000367188.5 | c.1886C>G | p.Ser629Cys | missense_variant | 1/2 | 1 | NM_032833.5 | P1 | |
PPP1R15B-AS1 | ENST00000443515.1 | n.147-25811G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00413 AC: 628AN: 152150Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00108 AC: 271AN: 250202Hom.: 0 AF XY: 0.000688 AC XY: 93AN XY: 135224
GnomAD4 exome AF: 0.000481 AC: 703AN: 1460892Hom.: 9 Cov.: 32 AF XY: 0.000381 AC XY: 277AN XY: 726686
GnomAD4 genome AF: 0.00413 AC: 629AN: 152268Hom.: 7 Cov.: 32 AF XY: 0.00419 AC XY: 312AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 23, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | PPP1R15B: BP4, BS1, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 06, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at