15-64156050-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000942.5(PPIB):c.624G>A(p.Glu208Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,614,104 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_000942.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPIB | NM_000942.5 | c.624G>A | p.Glu208Glu | synonymous_variant | Exon 5 of 5 | ENST00000300026.4 | NP_000933.1 | |
SNX22 | NM_024798.3 | c.*1542C>T | 3_prime_UTR_variant | Exon 7 of 7 | ENST00000325881.9 | NP_079074.2 | ||
SNX22 | XM_017022581.2 | c.*1542C>T | 3_prime_UTR_variant | Exon 6 of 6 | XP_016878070.1 | |||
SNX22 | NR_073534.2 | n.2216C>T | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPIB | ENST00000300026.4 | c.624G>A | p.Glu208Glu | synonymous_variant | Exon 5 of 5 | 1 | NM_000942.5 | ENSP00000300026.4 | ||
SNX22 | ENST00000325881.9 | c.*1542C>T | 3_prime_UTR_variant | Exon 7 of 7 | 1 | NM_024798.3 | ENSP00000323435.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249634Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135090
GnomAD4 exome AF: 0.000129 AC: 188AN: 1461888Hom.: 0 Cov.: 30 AF XY: 0.000129 AC XY: 94AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
PPIB-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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at