5-123028777-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000943.5(PPIC):c.323G>A(p.Gly108Glu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000943.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPIC | NM_000943.5 | c.323G>A | p.Gly108Glu | missense_variant, splice_region_variant | 3/5 | ENST00000306442.5 | |
SNX24 | XM_017009395.2 | c.349-461C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIC | ENST00000306442.5 | c.323G>A | p.Gly108Glu | missense_variant, splice_region_variant | 3/5 | 1 | NM_000943.5 | P1 | |
PPIC | ENST00000415659.2 | n.859G>A | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
SNX24 | ENST00000502387.5 | n.384-461C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
SNX24 | ENST00000510914.5 | n.420-461C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.