rs144817614

Positions:

chr16-2100209-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001009944.3(PKD1):c.9669G>A(p.Thr3223=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00425 in 1,610,124 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 43 hom., cov: 32)

Exomes 𝑓: 0.0031 ( 56 hom. )

Consequence

PKD1
NM_001009944.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -4.42

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=-0.62).

BP6

Variant 16-2100209-C-T is Benign according to our data. Variant chr16-2100209-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 257044.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2100209-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-4.42 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0149 (2272/152328) while in subpopulation AFR AF= 0.0389 (1617/41588). AF 95% confidence interval is 0.0373. There are 43 homozygotes in gnomad4. There are 1161 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2272 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKD1	NM_001009944.3 linkuse as main transcript	c.9669G>A	p.Thr3223=	synonymous_variant	28/46	ENST00000262304.9	NP_001009944.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD1	ENST00000262304.9 linkuse as main transcript	c.9669G>A	p.Thr3223=	synonymous_variant	28/46	1	NM_001009944.3	ENSP00000262304	P5	P98161-1

Frequencies

GnomAD3 genomes

AF:

0.0149

AC:

2267

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0389

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0251

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00197

Gnomad OTH

AF:

0.0191

GnomAD3 exomes

AF:

0.00580

AC:

1420

AN:

244826

Hom.:

AF XY:

0.00502

AC XY:

672

AN XY:

133826

show subpopulations

Gnomad AFR exome

AF:

0.0375

Gnomad AMR exome

AF:

0.0102

Gnomad ASJ exome

AF:

0.0191

Gnomad EAS exome

AF:

0.000220

Gnomad SAS exome

AF:

0.000164

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00245

Gnomad OTH exome

AF:

0.00866

GnomAD4 exome

AF:

0.00314

AC:

4572

AN:

1457796

Hom.:

Cov.:

AF XY:

0.00295

AC XY:

2136

AN XY:

725244

show subpopulations

Gnomad4 AFR exome

AF:

0.0390

Gnomad4 AMR exome

AF:

0.0108

Gnomad4 ASJ exome

AF:

0.0183

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000151

Gnomad4 FIN exome

AF:

0.0000576

Gnomad4 NFE exome

AF:

0.00156

Gnomad4 OTH exome

AF:

0.00763

GnomAD4 genome

AF:

0.0149

AC:

2272

AN:

152328

Hom.:

Cov.:

AF XY:

0.0156

AC XY:

1161

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0389

Gnomad4 AMR

AF:

0.0250

Gnomad4 ASJ

AF:

0.0173

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00197

Gnomad4 OTH

AF:

0.0189

Alfa

AF:

0.00783

Hom.:

Bravo

AF:

0.0172

EpiCase

AF:

0.00289

EpiControl

AF:

0.00320

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 25, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 30, 2019	This variant is associated with the following publications: (PMID: 29860066, 22383692, 17574468, 11967008, 11115377, 10923040) -

Polycystic kidney disease, adult type

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jul 23, 2021	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Feb 21, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Polycystic kidney disease

Benign:1

Benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

The PKD1 p.Thr3223Thr variant was identified in 7 of 970 proband chromosomes (frequency: 0.007) from individuals or families with ADPKD (Rossetti 2001, Rossetti 2002, Rossetti 2012, Garcia-Gonzalez 2007). In all these studies, the variant was identified as a polymorphism, and in one study occurring in the homozygous state, frequency unspecified (Koptides 2000). The variant was identified in dbSNP (ID:rs144817614) as â€šÃ„ÃºNAâ€šÃ„Ã¹, ADPKD Mutation Database (as Likely Neutral), but not in the Clinvitae, ClinVar, GeneInsight COGR, MutDB, PKD1-LOVD, and PKD1-LOVD 3.0 databases. This variant was also identified in the 1000 Genomes Project in 79 of 5000 chromosomes (frequency: 0.0158), HAPMAP populations: EAS in 2 of 1008 chromosomes (frequency: 0.002)/EUR in 7 of 1006 chromosomes (frequency: 0.007), in NHLBI GO Exome Sequencing Project in 15 of 5384 European American alleles (frequency: 0.00279) and in 89 of 3000 African American alleles (frequency: 0.02967), and in the Exome Aggregation Consortium database (March 14, 2016) in 615 of 113462 chromosomes (freq. 0.00542) in the following populations: African in 328 (8 homozygous) of 8492 chromosomes (freq. 0.03862), Other in 9 of 852 chromosomes (freq. 0.01056), Latino in 83 of 11316 chromosomes (freq. 0.000734), European (Non-Finnish) in 192 of 61484 chromosomes (freq. 0.00312), Finnish in 1 of 6518 chromosomes (freq. 0.00015) and East Asian in 1 of 8362 chromosomes (freq. 0.0001) and South Asian in 1 of 16438 chromosomes (freq. 0.00006), however we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. The p.Thr3223Thr variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, this variant is classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

0.078

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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