1-204409544-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032833.5(PPP1R15B):āc.1868T>Cā(p.Val623Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032833.5 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 |
---|---|---|---|---|---|---|---|
PPP1R15B | NM_032833.5 | c.1868T>C | p.Val623Ala | missense_variant | 1/2 | ENST00000367188.5 | |
PPP1R15B | XM_005245551.6 | c.1868T>C | p.Val623Ala | missense_variant | 1/3 | ||
PPP1R15B | XM_047432518.1 | c.1868T>C | p.Val623Ala | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R15B | ENST00000367188.5 | c.1868T>C | p.Val623Ala | missense_variant | 1/2 | 1 | NM_032833.5 | P1 | |
PPP1R15B-AS1 | ENST00000443515.1 | n.147-25793A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251360Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135874
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727220
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74490
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.1868T>C (p.V623A) alteration is located in exon 1 (coding exon 1) of the PPP1R15B gene. This alteration results from a T to C substitution at nucleotide position 1868, causing the valine (V) at amino acid position 623 to be replaced by an alanine (A). 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