Variant 16-81179773-A-G 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.2132T>C(p.Leu711Pro) variant causes a missense change. The variant allele was found at a frequency of 0.825 in 1,613,554 control chromosomes in the GnomAD database, including 550,541 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 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 0.80 ( 49203 hom., cov: 31)

Exomes 𝑓: 0.83 ( 501338 hom. )

Consequence

PKD1L2
ENST00000525539.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.75

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:

PKD1L2 (HGNC:):

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=8.4988994E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 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.2147T>C		non_coding_transcript_exon_variant	13/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD1L2	ENST00000525539.5 linkuse as main transcript	c.2132T>C	p.Leu711Pro	missense_variant	13/43	1		ENSP00000434417.1

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

121775

AN:

151936

Hom.:

49174

Cov.:

show subpopulations

Gnomad AFR

AF:

0.721

Gnomad AMI

AF:

0.888

Gnomad AMR

AF:

0.800

Gnomad ASJ

AF:

0.808

Gnomad EAS

AF:

0.966

Gnomad SAS

AF:

0.751

Gnomad FIN

AF:

0.855

Gnomad MID

AF:

0.835

Gnomad NFE

AF:

0.832

Gnomad OTH

AF:

0.811

GnomAD3 exomes

AF:

0.821

AC:

204488

AN:

249036

Hom.:

84468

AF XY:

0.821

AC XY:

110853

AN XY:

135084

show subpopulations

Gnomad AFR exome

AF:

0.715

Gnomad AMR exome

AF:

0.795

Gnomad ASJ exome

AF:

0.822

Gnomad EAS exome

AF:

0.964

Gnomad SAS exome

AF:

0.751

Gnomad FIN exome

AF:

0.857

Gnomad NFE exome

AF:

0.833

Gnomad OTH exome

AF:

0.820

GnomAD4 exome

AF:

0.827

AC:

1208980

AN:

1461500

Hom.:

501338

Cov.:

AF XY:

0.826

AC XY:

600393

AN XY:

727040

show subpopulations

Gnomad4 AFR exome

AF:

0.720

Gnomad4 AMR exome

AF:

0.800

Gnomad4 ASJ exome

AF:

0.817

Gnomad4 EAS exome

AF:

0.966

Gnomad4 SAS exome

AF:

0.758

Gnomad4 FIN exome

AF:

0.859

Gnomad4 NFE exome

AF:

0.831

Gnomad4 OTH exome

AF:

0.821

GnomAD4 genome

AF:

0.801

AC:

121854

AN:

152054

Hom.:

49203

Cov.:

AF XY:

0.803

AC XY:

59693

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.721

Gnomad4 AMR

AF:

0.800

Gnomad4 ASJ

AF:

0.808

Gnomad4 EAS

AF:

0.966

Gnomad4 SAS

AF:

0.752

Gnomad4 FIN

AF:

0.855

Gnomad4 NFE

AF:

0.832

Gnomad4 OTH

AF:

0.810

Alfa

AF:

0.831

Hom.:

117245

Bravo

AF:

0.800

TwinsUK

AF:

0.835

AC:

3098

ALSPAC

AF:

0.826

AC:

3185

ESP6500AA

AF:

0.728

AC:

2840

ESP6500EA

AF:

0.835

AC:

6931

ExAC

AF:

0.819

AC:

98980

Asia WGS

AF:

0.843

AC:

2929

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.12

Eigen

Benign

-0.66

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.012

LIST_S2

Benign

0.14

T;T;T

MetaRNN

Benign

8.5e-7

T;T;T

MetaSVM

Benign

-0.94

PrimateAI

Benign

0.41

PROVEAN

Benign

4.5

N;N;N

REVEL

Benign

0.26

Polyphen

0.0

.;B;B

Vest4

0.18

MPC

.;.;4.19142513741E-4

ClinPred

0.0036

GERP RS

5.0

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