Variant rs7191351 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.359A>T(p.Gln120Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 1,613,750 control chromosomes in the GnomAD database, including 291,473 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 0.55 ( 23978 hom., cov: 33)

Exomes 𝑓: 0.60 ( 267495 hom. )

Consequence

PKD1L2
ENST00000525539.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

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=1.1443923E-5).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 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.383A>T		non_coding_transcript_exon_variant	2/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD1L2	ENST00000525539.5 linkuse as main transcript	c.359A>T	p.Gln120Leu	missense_variant	2/43	1		ENSP00000434417

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83940

AN:

152014

Hom.:

23971

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.723

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.574

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.616

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.585

GnomAD3 exomes

AF:

0.552

AC:

137613

AN:

249172

Hom.:

39252

AF XY:

0.554

AC XY:

74873

AN XY:

135220

show subpopulations

Gnomad AFR exome

AF:

0.420

Gnomad AMR exome

AF:

0.475

Gnomad ASJ exome

AF:

0.590

Gnomad EAS exome

AF:

0.418

Gnomad SAS exome

AF:

0.419

Gnomad FIN exome

AF:

0.603

Gnomad NFE exome

AF:

0.635

Gnomad OTH exome

AF:

0.606

GnomAD4 exome

AF:

0.600

AC:

876936

AN:

1461618

Hom.:

267495

Cov.:

AF XY:

0.596

AC XY:

433137

AN XY:

727098

show subpopulations

Gnomad4 AFR exome

AF:

0.413

Gnomad4 AMR exome

AF:

0.484

Gnomad4 ASJ exome

AF:

0.587

Gnomad4 EAS exome

AF:

0.391

Gnomad4 SAS exome

AF:

0.420

Gnomad4 FIN exome

AF:

0.602

Gnomad4 NFE exome

AF:

0.632

Gnomad4 OTH exome

AF:

0.586

GnomAD4 genome

AF:

0.552

AC:

83966

AN:

152132

Hom.:

23978

Cov.:

AF XY:

0.549

AC XY:

40827

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.423

Gnomad4 AMR

AF:

0.554

Gnomad4 ASJ

AF:

0.574

Gnomad4 EAS

AF:

0.409

Gnomad4 SAS

AF:

0.411

Gnomad4 FIN

AF:

0.616

Gnomad4 NFE

AF:

0.636

Gnomad4 OTH

AF:

0.583

Alfa

AF:

0.610

Hom.:

20112

Bravo

AF:

0.546

TwinsUK

AF:

0.632

AC:

2344

ALSPAC

AF:

0.635

AC:

2448

ESP6500AA

AF:

0.458

AC:

1866

ESP6500EA

AF:

0.633

AC:

5288

ExAC

AF:

0.551

AC:

66566

Asia WGS

AF:

0.475

AC:

1653

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.95

Eigen

Benign

-0.59

Eigen_PC

Benign

-0.69

FATHMM_MKL

Benign

0.49

LIST_S2

Benign

0.43

MetaRNN

Benign

0.000011

MetaSVM

Benign

-0.99

MutationTaster

Benign

1.0

PrimateAI

Benign

0.28

PROVEAN

Uncertain

-3.9

REVEL

Benign

0.086

Polyphen

0.76

Vest4

0.48

ClinPred

0.033

GERP RS

1.4

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