Variant rs143936796 details in Genebe, Genetics Data Aggregator

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

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 3.49

Variant links:

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]

PRKCSH links:

Genome browser will be placed here

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 GnomAd4 at 4443 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKCSH	NM_001289104.2 linkuse as main transcript	c.79+10_79+12del		splice_donor_region_variant, intron_variant		ENST00000677123.1	NP_001276033.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKCSH	ENST00000677123.1 linkuse as main transcript	c.79+10_79+12del		splice_donor_region_variant, intron_variant			NM_001289104.2	ENSP00000503163	A2

Frequencies

GnomAD3 genomes

AF:

0.0298

AC:

4441

AN:

148980

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00707

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0319

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.0884

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0379

Gnomad OTH

AF:

0.0179

GnomAD3 exomes

AF:

0.0354

AC:

7147

AN:

201694

Hom.:

189

AF XY:

0.0342

AC XY:

3738

AN XY:

109450

show subpopulations

Gnomad AFR exome

AF:

0.00612

Gnomad AMR exome

AF:

0.0588

Gnomad ASJ exome

AF:

0.0115

Gnomad EAS exome

AF:

0.0000678

Gnomad SAS exome

AF:

0.0153

Gnomad FIN exome

AF:

0.0820

Gnomad NFE exome

AF:

0.0374

Gnomad OTH exome

AF:

0.0250

GnomAD4 exome

AF:

0.0374

AC:

53590

AN:

1434338

Hom.:

1200

AF XY:

0.0361

AC XY:

25733

AN XY:

712028

show subpopulations

Gnomad4 AFR exome

AF:

0.00584

Gnomad4 AMR exome

AF:

0.0519

Gnomad4 ASJ exome

AF:

0.0111

Gnomad4 EAS exome

AF:

0.0000263

Gnomad4 SAS exome

AF:

0.0162

Gnomad4 FIN exome

AF:

0.0774

Gnomad4 NFE exome

AF:

0.0399

Gnomad4 OTH exome

AF:

0.0320

GnomAD4 genome

AF:

0.0298

AC:

4443

AN:

149084

Hom.:

Cov.:

AF XY:

0.0324

AC XY:

2360

AN XY:

72944

show subpopulations

Gnomad4 AFR

AF:

0.00705

Gnomad4 AMR

AF:

0.0319

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.0158

Gnomad4 FIN

AF:

0.0884

Gnomad4 NFE

AF:

0.0379

Gnomad4 OTH

AF:

0.0178

Alfa

AF:

0.0304

Hom.:

Bravo

AF:

0.0256

Asia WGS

AF:

0.00577

AC:

AN:

3478

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

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over