chr19-11436201-GTCC-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001289104.2(PRKCSH):c.79+10_79+12del variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 1,583,422 control chromosomes in the GnomAD database, including 1,282 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.030 ( 82 hom., cov: 32)
Exomes 𝑓: 0.037 ( 1200 hom. )
Consequence
PRKCSH
NM_001289104.2 splice_donor_region, intron
NM_001289104.2 splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.49
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 Benign. Variant got -16 ACMG points.
BP6
?
Variant 19-11436201-GTCC-G is Benign according to our data. Variant chr19-11436201-GTCC-G is described in ClinVar as [Benign]. Clinvar id is 94077.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0298 (4443/149084) while in subpopulation NFE AF= 0.0379 (2576/67996). AF 95% confidence interval is 0.0367. There are 82 homozygotes in gnomad4. There are 2360 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 4441 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCSH | NM_001289104.2 | c.79+10_79+12del | splice_donor_region_variant, intron_variant | ENST00000677123.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCSH | ENST00000677123.1 | c.79+10_79+12del | splice_donor_region_variant, intron_variant | NM_001289104.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0298 AC: 4441AN: 148980Hom.: 82 Cov.: 32
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GnomAD3 exomes AF: 0.0354 AC: 7147AN: 201694Hom.: 189 AF XY: 0.0342 AC XY: 3738AN XY: 109450
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GnomAD4 exome AF: 0.0374 AC: 53590AN: 1434338Hom.: 1200 AF XY: 0.0361 AC XY: 25733AN XY: 712028
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GnomAD4 genome ? AF: 0.0298 AC: 4443AN: 149084Hom.: 82 Cov.: 32 AF XY: 0.0324 AC XY: 2360AN XY: 72944
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 10, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Polycystic liver disease 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at