19-11447525-AGAGGAGGAGGAGGAGGAG-AGAGGAGGAGGAGGAGGAGGAGGAGGAG
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP3BS1_SupportingBS2
The NM_001289104.2(PRKCSH):c.960_968dup(p.Glu323_Glu325dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T312T) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.00065 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00068 ( 0 hom. )
Consequence
PRKCSH
NM_001289104.2 inframe_insertion
NM_001289104.2 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.52
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 -6 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001289104.2
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000655 (98/149626) while in subpopulation NFE AF= 0.000965 (65/67348). AF 95% confidence interval is 0.000776. There are 0 homozygotes in gnomad4. There are 44 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 98 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCSH | NM_001289104.2 | c.960_968dup | p.Glu323_Glu325dup | inframe_insertion | 11/18 | ENST00000677123.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCSH | ENST00000677123.1 | c.960_968dup | p.Glu323_Glu325dup | inframe_insertion | 11/18 | NM_001289104.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000655 AC: 98AN: 149518Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.000473 AC: 83AN: 175324Hom.: 0 AF XY: 0.000493 AC XY: 47AN XY: 95328
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GnomAD4 exome AF: 0.000679 AC: 974AN: 1434282Hom.: 0 Cov.: 0 AF XY: 0.000682 AC XY: 486AN XY: 712774
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GnomAD4 genome AF: 0.000655 AC: 98AN: 149626Hom.: 0 Cov.: 0 AF XY: 0.000604 AC XY: 44AN XY: 72902
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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 | Nov 27, 2023 | This variant, c.960_968dup, results in the insertion of 3 amino acid(s) of the PRKCSH protein (p.Glu323_Glu325dup), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at