Variant rs160841 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001289104.2(PRKCSH):c.1196+52A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 1,546,554 control chromosomes in the GnomAD database, including 9,045 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2743 hom., cov: 32)

Exomes 𝑓: 0.083 ( 6302 hom. )

Consequence

PRKCSH
NM_001289104.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0780

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 19-11448343-A-G is Benign according to our data. Variant chr19-11448343-A-G is described in ClinVar as [Benign]. Clinvar id is 1181148.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKCSH	NM_001289104.2 linkuse as main transcript	c.1196+52A>G		intron_variant		ENST00000677123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKCSH	ENST00000677123.1 linkuse as main transcript	c.1196+52A>G		intron_variant			NM_001289104.2	A2

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23766

AN:

151930

Hom.:

2729

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.168

Gnomad ASJ

AF:

0.0971

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.0869

Gnomad FIN

AF:

0.0806

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0750

Gnomad OTH

AF:

0.149

GnomAD3 exomes

AF:

0.116

AC:

19178

AN:

165672

Hom.:

1445

AF XY:

0.110

AC XY:

9662

AN XY:

87710

show subpopulations

Gnomad AFR exome

AF:

0.321

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.103

Gnomad EAS exome

AF:

0.164

Gnomad SAS exome

AF:

0.0955

Gnomad FIN exome

AF:

0.0857

Gnomad NFE exome

AF:

0.0725

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.0829

AC:

115536

AN:

1394504

Hom.:

6302

Cov.:

AF XY:

0.0826

AC XY:

56910

AN XY:

688996

show subpopulations

Gnomad4 AFR exome

AF:

0.323

Gnomad4 AMR exome

AF:

0.165

Gnomad4 ASJ exome

AF:

0.102

Gnomad4 EAS exome

AF:

0.131

Gnomad4 SAS exome

AF:

0.0959

Gnomad4 FIN exome

AF:

0.0824

Gnomad4 NFE exome

AF:

0.0686

Gnomad4 OTH exome

AF:

0.105

GnomAD4 genome

AF:

0.157

AC:

23839

AN:

152050

Hom.:

2743

Cov.:

AF XY:

0.156

AC XY:

11564

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.0971

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.0866

Gnomad4 FIN

AF:

0.0806

Gnomad4 NFE

AF:

0.0751

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.102

Hom.:

323

Bravo

AF:

0.172

Asia WGS

AF:

0.158

AC:

547

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

DANN

Benign

0.70

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