Variant rs8060294 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000525539.5(PKD1L2):c.518T>C(p.Leu173Ser) variant causes a missense change. The variant allele was found at a frequency of 0.309 in 1,608,088 control chromosomes in the GnomAD database, including 79,704 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10644 hom., cov: 31)

Exomes 𝑓: 0.30 ( 69060 hom. )

Consequence

PKD1L2
ENST00000525539.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.33

Variant links:

Genes affected

PKD1L2 (HGNC:21715): (polycystin 1 like 2 (gene/pseudogene)) This gene encodes a member of the polycystin protein family. This protein may function as a G-protein-coupled component or regulator of cation channel pores. The long isoform of this protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. This gene is a polymorphic pseudogene in humans. [provided by RefSeq, May 2022]

PKD1L2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.0650706E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKD1L2	NR_126532.3 linkuse as main transcript	n.542T>C		non_coding_transcript_exon_variant	3/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD1L2	ENST00000525539.5 linkuse as main transcript	c.518T>C	p.Leu173Ser	missense_variant	3/43	1		ENSP00000434417

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54451

AN:

151730

Hom.:

10632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.522

Gnomad AMI

AF:

0.307

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.401

Gnomad SAS

AF:

0.260

Gnomad FIN

AF:

0.326

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.320

GnomAD3 exomes

AF:

0.306

AC:

72906

AN:

238148

Hom.:

11689

AF XY:

0.299

AC XY:

38694

AN XY:

129576

show subpopulations

Gnomad AFR exome

AF:

0.522

Gnomad AMR exome

AF:

0.311

Gnomad ASJ exome

AF:

0.217

Gnomad EAS exome

AF:

0.412

Gnomad SAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.306

Gnomad NFE exome

AF:

0.278

Gnomad OTH exome

AF:

0.301

GnomAD4 exome

AF:

0.304

AC:

442713

AN:

1456240

Hom.:

69060

Cov.:

AF XY:

0.301

AC XY:

217593

AN XY:

723950

show subpopulations

Gnomad4 AFR exome

AF:

0.531

Gnomad4 AMR exome

AF:

0.311

Gnomad4 ASJ exome

AF:

0.213

Gnomad4 EAS exome

AF:

0.389

Gnomad4 SAS exome

AF:

0.266

Gnomad4 FIN exome

AF:

0.307

Gnomad4 NFE exome

AF:

0.298

Gnomad4 OTH exome

AF:

0.317

GnomAD4 genome

AF:

0.359

AC:

54527

AN:

151848

Hom.:

10644

Cov.:

AF XY:

0.358

AC XY:

26562

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.522

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.402

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.326

Gnomad4 NFE

AF:

0.287

Gnomad4 OTH

AF:

0.320

Alfa

AF:

0.285

Hom.:

11704

Bravo

AF:

0.371

TwinsUK

AF:

0.307

AC:

1138

ALSPAC

AF:

0.306

AC:

1180

ESP6500AA

AF:

0.507

AC:

1980

ESP6500EA

AF:

0.278

AC:

2300

ExAC

AF:

0.300

AC:

36191

Asia WGS

AF:

0.407

AC:

1415

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.97

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.55

FATHMM_MKL

Benign

0.048

LIST_S2

Benign

0.23

MetaRNN

Benign

0.00061

MetaSVM

Benign

-0.93

MutationTaster

Benign

0.96

PrimateAI

Benign

0.46

PROVEAN

Benign

3.5

REVEL

Benign

0.11

Polyphen

0.0

Vest4

0.15

ClinPred

0.0067

GERP RS

3.8

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over