chr17-50140208-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_032595.5(PPP1R9B):c.1751G>A(p.Arg584Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000483 in 1,449,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032595.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1R9B | ENST00000612501.2 | c.1751G>A | p.Arg584Gln | missense_variant | Exon 5 of 10 | 1 | NM_032595.5 | ENSP00000478767.1 | ||
PPP1R9B | ENST00000513579.1 | n.418G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | 3 | |||||
ENSG00000236472 | ENST00000451776.1 | n.208+2800C>T | intron_variant | Intron 2 of 3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000445 AC: 1AN: 224706Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121632
GnomAD4 exome AF: 0.00000483 AC: 7AN: 1449112Hom.: 0 Cov.: 31 AF XY: 0.00000556 AC XY: 4AN XY: 719662
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
PPP1R9B-related disorder Benign:1
This variant is classified as likely 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