Variant rs9935113 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000531391.5(PKD1L2):c.298G>T(p.Gly100Cys) variant causes a missense change. The variant allele was found at a frequency of 0.18 in 1,613,554 control chromosomes in the GnomAD database, including 27,320 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3148 hom., cov: 31)

Exomes 𝑓: 0.18 ( 24172 hom. )

Consequence

PKD1L2
ENST00000531391.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.19

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=0.001959771).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKD1L2	NR_126532.3 linkuse as main transcript	n.2368G>T		non_coding_transcript_exon_variant	14/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKD1L2	ENST00000525539.5 linkuse as main transcript	c.2353G>T	p.Gly785Cys	missense_variant	14/43	1

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29723

AN:

151780

Hom.:

3138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.0984

Gnomad SAS

AF:

0.260

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.189

GnomAD3 exomes

AF:

0.184

AC:

45775

AN:

248896

Hom.:

4570

AF XY:

0.185

AC XY:

24925

AN XY:

135094

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.204

Gnomad ASJ exome

AF:

0.173

Gnomad EAS exome

AF:

0.107

Gnomad SAS exome

AF:

0.257

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.168

Gnomad OTH exome

AF:

0.182

GnomAD4 exome

AF:

0.178

AC:

259960

AN:

1461656

Hom.:

24172

Cov.:

AF XY:

0.179

AC XY:

130391

AN XY:

727140

show subpopulations

Gnomad4 AFR exome

AF:

0.257

Gnomad4 AMR exome

AF:

0.199

Gnomad4 ASJ exome

AF:

0.180

Gnomad4 EAS exome

AF:

0.0747

Gnomad4 SAS exome

AF:

0.251

Gnomad4 FIN exome

AF:

0.142

Gnomad4 NFE exome

AF:

0.174

Gnomad4 OTH exome

AF:

0.185

GnomAD4 genome

AF:

0.196

AC:

29754

AN:

151898

Hom.:

3148

Cov.:

AF XY:

0.194

AC XY:

14364

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.258

Gnomad4 AMR

AF:

0.196

Gnomad4 ASJ

AF:

0.190

Gnomad4 EAS

AF:

0.0980

Gnomad4 SAS

AF:

0.259

Gnomad4 FIN

AF:

0.143

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.172

Hom.:

5764

Bravo

AF:

0.197

TwinsUK

AF:

0.169

AC:

628

ALSPAC

AF:

0.179

AC:

690

ESP6500AA

AF:

0.247

AC:

1011

ESP6500EA

AF:

0.168

AC:

1412

ExAC

AF:

0.185

AC:

22322

Asia WGS

AF:

0.182

AC:

635

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Uncertain

0.020

CADD

Uncertain

DANN

Uncertain

1.0

Eigen

Benign

0.084

Eigen_PC

Benign

0.078

FATHMM_MKL

Uncertain

0.77

LIST_S2

Benign

0.75

T;T

MetaRNN

Benign

0.0020

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

0.63

P;P;P

PrimateAI

Benign

0.42

PROVEAN

Pathogenic

-8.2

D;D

REVEL

Pathogenic

0.71

Polyphen

1.0

.;D

Vest4

0.82

ClinPred

0.092

GERP RS

4.9

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