chr1-204409647-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032833.5(PPP1R15B):c.1765A>G(p.Lys589Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 1,613,680 control chromosomes in the GnomAD database, including 467 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_032833.5 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 |
---|---|---|---|---|---|---|---|
PPP1R15B | NM_032833.5 | c.1765A>G | p.Lys589Glu | missense_variant | 1/2 | ENST00000367188.5 | |
PPP1R15B | XM_005245551.6 | c.1765A>G | p.Lys589Glu | missense_variant | 1/3 | ||
PPP1R15B | XM_047432518.1 | c.1765A>G | p.Lys589Glu | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R15B | ENST00000367188.5 | c.1765A>G | p.Lys589Glu | missense_variant | 1/2 | 1 | NM_032833.5 | P1 | |
PPP1R15B-AS1 | ENST00000443515.1 | n.147-25690T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0153 AC: 2334AN: 152094Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.0192 AC: 4839AN: 251472Hom.: 84 AF XY: 0.0214 AC XY: 2908AN XY: 135914
GnomAD4 exome AF: 0.0219 AC: 31938AN: 1461468Hom.: 447 Cov.: 32 AF XY: 0.0228 AC XY: 16595AN XY: 727054
GnomAD4 genome ? AF: 0.0153 AC: 2333AN: 152212Hom.: 20 Cov.: 32 AF XY: 0.0154 AC XY: 1146AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at