rs74331768

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001009944.3(PKD1):c.3375C>T(p.Ser1125Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0993 in 1,608,554 control chromosomes in the GnomAD database, including 9,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1949 hom., cov: 33)

Exomes 𝑓: 0.095 ( 7725 hom. )

Consequence

PKD1
NM_001009944.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.657

Variant links:

Genes affected

PKD1 (HGNC:9008): (polycystin 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways. It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been described. [provided by RefSeq, Oct 2008]

PKD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 16-2111792-G-A is Benign according to our data. Variant chr16-2111792-G-A is described in ClinVar as [Benign]. Clinvar id is 256950.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2111792-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=0.657 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKD1	NM_001009944.3 link	c.3375C>T	p.Ser1125Ser	synonymous_variant	Exon 15 of 46	ENST00000262304.9	NP_001009944.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKD1	ENST00000262304.9 link	c.3375C>T	p.Ser1125Ser	synonymous_variant	Exon 15 of 46	1	NM_001009944.3	ENSP00000262304.4		P98161-1

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21059

AN:

152028

Hom.:

1946

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0280

Gnomad FIN

AF:

0.0759

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0979

Gnomad OTH

AF:

0.147

GnomAD3 exomes

AF:

0.0886

AC:

21360

AN:

241154

Hom.:

1337

AF XY:

0.0845

AC XY:

11124

AN XY:

131620

show subpopulations

Gnomad AFR exome

AF:

0.269

Gnomad AMR exome

AF:

0.0699

Gnomad ASJ exome

AF:

0.141

Gnomad EAS exome

AF:

0.0000558

Gnomad SAS exome

AF:

0.0291

Gnomad FIN exome

AF:

0.0731

Gnomad NFE exome

AF:

0.0975

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.0951

AC:

138572

AN:

1456408

Hom.:

7725

Cov.:

AF XY:

0.0932

AC XY:

67504

AN XY:

724396

show subpopulations

Gnomad4 AFR exome

AF:

0.270

Gnomad4 AMR exome

AF:

0.0773

Gnomad4 ASJ exome

AF:

0.143

Gnomad4 EAS exome

AF:

0.0000757

Gnomad4 SAS exome

AF:

0.0317

Gnomad4 FIN exome

AF:

0.0703

Gnomad4 NFE exome

AF:

0.0982

Gnomad4 OTH exome

AF:

0.103

GnomAD4 genome

AF:

0.139

AC:

21089

AN:

152146

Hom.:

1949

Cov.:

AF XY:

0.133

AC XY:

9888

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.260

Gnomad4 AMR

AF:

0.111

Gnomad4 ASJ

AF:

0.150

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0276

Gnomad4 FIN

AF:

0.0759

Gnomad4 NFE

AF:

0.0979

Gnomad4 OTH

AF:

0.145

Alfa

AF:

0.117

Hom.:

437

Bravo

AF:

0.150

Asia WGS

AF:

0.0300

AC:

107

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Feb 01, 2017

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 04, 2021

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Sep 25, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 11967008) -

Polycystic kidney disease, adult type

Benign:1

Jul 07, 2020

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Polycystic kidney disease

Benign:1

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

The PKD1, p.Ser1125Servariant was identified in 10.8% of 95064 control alleles in the Exome Aggregation Consortium (March 14, 2016). This variant was identified by our laboratory with a co-occurring pathogenic PKD1 variant (c.11798_11810del, p.Leu3933ArgfsX8), in a patient with PKD increasing the likelihood that the p.Ala3512Val variant does not have clinical significance. According to ACMG guidelines for variant classification based on allele frequency, category BA1, this variant is considered benign and has not been further reviewed (Richards 2015). -

Autosomal dominant polycystic kidney disease

Benign:1

Jan 01, 2019

Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.51

DANN

Benign

0.79

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