chr19-11436202-T-TCCTCCTGTTCAC
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001289104.2(PRKCSH):c.79+12_79+23dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00491 in 1,474,422 control chromosomes in the GnomAD database, including 344 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.027 ( 190 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 154 hom. )
Consequence
PRKCSH
NM_001289104.2 splice_region, intron
NM_001289104.2 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.947
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 19-11436202-T-TCCTCCTGTTCAC is Benign according to our data. Variant chr19-11436202-T-TCCTCCTGTTCAC is described in ClinVar as [Benign]. Clinvar id is 769958.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.086 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCSH | NM_001289104.2 | c.79+12_79+23dup | splice_region_variant, intron_variant | ENST00000677123.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCSH | ENST00000677123.1 | c.79+12_79+23dup | splice_region_variant, intron_variant | NM_001289104.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0265 AC: 3788AN: 143162Hom.: 188 Cov.: 32
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GnomAD3 exomes AF: 0.00517 AC: 1046AN: 202150Hom.: 50 AF XY: 0.00361 AC XY: 395AN XY: 109442
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GnomAD4 exome AF: 0.00259 AC: 3444AN: 1331146Hom.: 154 Cov.: 30 AF XY: 0.00214 AC XY: 1420AN XY: 662180
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GnomAD4 genome ? AF: 0.0265 AC: 3798AN: 143276Hom.: 190 Cov.: 32 AF XY: 0.0255 AC XY: 1779AN XY: 69672
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 18, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at