Variant rs7185774 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.386G>A(p.Gly129Asp) variant causes a missense change. The variant allele was found at a frequency of 0.298 in 1,613,732 control chromosomes in the GnomAD database, including 78,090 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 0.25 ( 5902 hom., cov: 33)

Exomes 𝑓: 0.30 ( 72188 hom. )

Consequence

PKD1L2
ENST00000525539.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.28

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=0.0021229684).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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.410G>A		non_coding_transcript_exon_variant	2/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKD1L2	ENST00000525539.5 linkuse as main transcript	c.386G>A	p.Gly129Asp	missense_variant	2/43	1

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38478

AN:

152024

Hom.:

5905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.00734

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.301

GnomAD3 exomes

AF:

0.260

AC:

64940

AN:

249314

Hom.:

10386

AF XY:

0.266

AC XY:

36042

AN XY:

135272

show subpopulations

Gnomad AFR exome

AF:

0.106

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.375

Gnomad EAS exome

AF:

0.00590

Gnomad SAS exome

AF:

0.153

Gnomad FIN exome

AF:

0.295

Gnomad NFE exome

AF:

0.357

Gnomad OTH exome

AF:

0.317

GnomAD4 exome

AF:

0.303

AC:

442269

AN:

1461590

Hom.:

72188

Cov.:

AF XY:

0.301

AC XY:

218840

AN XY:

727094

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.186

Gnomad4 ASJ exome

AF:

0.376

Gnomad4 EAS exome

AF:

0.00300

Gnomad4 SAS exome

AF:

0.155

Gnomad4 FIN exome

AF:

0.295

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.253

AC:

38470

AN:

152142

Hom.:

5902

Cov.:

AF XY:

0.248

AC XY:

18433

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.252

Gnomad4 ASJ

AF:

0.362

Gnomad4 EAS

AF:

0.00736

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.288

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.309

Hom.:

5236

Bravo

AF:

0.244

TwinsUK

AF:

0.326

AC:

1207

ALSPAC

AF:

0.329

AC:

1269

ESP6500AA

AF:

0.116

AC:

481

ESP6500EA

AF:

0.346

AC:

2910

ExAC

AF:

0.263

AC:

31796

Asia WGS

AF:

0.0830

AC:

291

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

CADD

Benign

DANN

Uncertain

1.0

Eigen

Uncertain

0.45

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.52

MetaRNN

Benign

0.0021

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.17

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-3.8

REVEL

Benign

0.28

Polyphen

1.0

Vest4

0.79

ClinPred

0.015

GERP RS

5.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over