chr19-11447525-AGAGGAGGAGGAGGAG-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001289104.2(PRKCSH):βc.954_968delβ(p.Glu321_Glu325del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000152 in 1,583,934 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β ).
Frequency
Genomes: π 0.00016 ( 0 hom., cov: 0)
Exomes π: 0.00015 ( 0 hom. )
Consequence
PRKCSH
NM_001289104.2 inframe_deletion
NM_001289104.2 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.27
Genes affected
PRKCSH (HGNC:9411): (PRKCSH beta subunit of glucosidase II) This gene encodes the beta-subunit of glucosidase II, an N-linked glycan-processing enzyme in the endoplasmic reticulum. The encoded protein is an acidic phosphoprotein known to be a substrate for protein kinase C. Mutations in this gene have been associated with the autosomal dominant polycystic liver disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001289104.2
BS2
High AC in GnomAd4 at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCSH | NM_001289104.2 | c.954_968del | p.Glu321_Glu325del | inframe_deletion | 11/18 | ENST00000677123.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCSH | ENST00000677123.1 | c.954_968del | p.Glu321_Glu325del | inframe_deletion | 11/18 | NM_001289104.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000161 AC: 24AN: 149516Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000151 AC: 217AN: 1434310Hom.: 0 AF XY: 0.000146 AC XY: 104AN XY: 712786
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GnomAD4 genome AF: 0.000160 AC: 24AN: 149624Hom.: 0 Cov.: 0 AF XY: 0.000165 AC XY: 12AN XY: 72900
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 22, 2023 | This variant, c.954_968del, results in the deletion of 5 amino acid(s) of the PRKCSH protein (p.Glu321_Glu325del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PRKCSH-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at