chr16-2114323-C-T

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.2700G>A(p.Pro900Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 1,610,282 control chromosomes in the GnomAD database, including 3,501 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.050 ( 271 hom., cov: 33)

Exomes 𝑓: 0.063 ( 3230 hom. )

Consequence

PKD1
NM_001009944.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -4.44

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=-0.84).

BP6

Variant 16-2114323-C-T is Benign according to our data. Variant chr16-2114323-C-T is described in ClinVar as [Benign]. Clinvar id is 256936.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2114323-C-T is described in Lovd as [Benign]. Variant chr16-2114323-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-4.44 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKD1	NM_001009944.3 link	c.2700G>A	p.Pro900Pro	synonymous_variant	Exon 11 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.2700G>A	p.Pro900Pro	synonymous_variant	Exon 11 of 46	1	NM_001009944.3	ENSP00000262304.4		P98161-1

Frequencies

GnomAD3 genomes

AF:

0.0499

AC:

7589

AN:

152220

Hom.:

271

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0128

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0478

Gnomad ASJ

AF:

0.0772

Gnomad EAS

AF:

0.000964

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0660

Gnomad OTH

AF:

0.0492

GnomAD3 exomes

AF:

0.0546

AC:

13552

AN:

248098

Hom.:

473

AF XY:

0.0564

AC XY:

7606

AN XY:

134900

show subpopulations

Gnomad AFR exome

AF:

0.0103

Gnomad AMR exome

AF:

0.0289

Gnomad ASJ exome

AF:

0.0860

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0417

Gnomad FIN exome

AF:

0.112

Gnomad NFE exome

AF:

0.0672

Gnomad OTH exome

AF:

0.0606

GnomAD4 exome

AF:

0.0634

AC:

92367

AN:

1457944

Hom.:

3230

Cov.:

AF XY:

0.0631

AC XY:

45735

AN XY:

725310

show subpopulations

Gnomad4 AFR exome

AF:

0.0103

Gnomad4 AMR exome

AF:

0.0295

Gnomad4 ASJ exome

AF:

0.0881

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.0416

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.0676

Gnomad4 OTH exome

AF:

0.0584

GnomAD4 genome

AF:

0.0498

AC:

7585

AN:

152338

Hom.:

271

Cov.:

AF XY:

0.0527

AC XY:

3923

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.0128

Gnomad4 AMR

AF:

0.0478

Gnomad4 ASJ

AF:

0.0772

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.0435

Gnomad4 FIN

AF:

0.115

Gnomad4 NFE

AF:

0.0660

Gnomad4 OTH

AF:

0.0487

Alfa

AF:

0.0529

Hom.:

Bravo

AF:

0.0417

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.0674

EpiControl

AF:

0.0618

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Polycystic kidney disease, adult type

Benign:2

Jun 09, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 22, 2020

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

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

- -

Oct 03, 2019

GeneDx

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 c.2700G>A, p.Pro900Pro variant was identified in 5.5% of 6402 control alleles in the Exome Aggregation Consortium (March 14, 2016). 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

-0.84

CADD

Benign

0.11

DANN

Benign

0.65

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

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