Variant rs12597040 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBA1

The ENST00000525539.5(PKD1L2):c.3107T>C(p.Leu1036Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,452,888 control chromosomes in the GnomAD database, including 85,572 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.31 ( 7873 hom., cov: 34)

Exomes 𝑓: 0.30 ( 77699 hom. )

Consequence

PKD1L2
ENST00000525539.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.284

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.11).

BP6

Variant 16-81165950-A-G is Benign according to our data. Variant chr16-81165950-A-G is described in ClinVar as [Benign]. Clinvar id is 2788471.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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.3122T>C		non_coding_transcript_exon_variant	19/43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein
PKD1L2	ENST00000525539.5 linkuse as main transcript	c.3107T>C	p.Leu1036Pro	missense_variant	19/43	1	ENSP00000434417
PKD1L2	ENST00000533478.5 linkuse as main transcript	c.1052T>C	p.Leu351Pro	missense_variant	8/32	1	ENSP00000434644
PKD1L2	ENST00000299598.11 linkuse as main transcript	n.1436T>C		non_coding_transcript_exon_variant	10/25	5

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46479

AN:

151846

Hom.:

7863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.364

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.296

GnomAD3 exomes

AF:

0.303

AC:

53998

AN:

178408

Hom.:

12781

AF XY:

0.297

AC XY:

28444

AN XY:

95714

show subpopulations

Gnomad AFR exome

AF:

0.186

Gnomad AMR exome

AF:

0.421

Gnomad ASJ exome

AF:

0.141

Gnomad EAS exome

AF:

0.664

Gnomad SAS exome

AF:

0.375

Gnomad FIN exome

AF:

0.323

Gnomad NFE exome

AF:

0.232

Gnomad OTH exome

AF:

0.253

GnomAD4 exome

AF:

0.302

AC:

392509

AN:

1300924

Hom.:

77699

Cov.:

AF XY:

0.304

AC XY:

196396

AN XY:

646636

show subpopulations

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.419

Gnomad4 ASJ exome

AF:

0.201

Gnomad4 EAS exome

AF:

0.679

Gnomad4 SAS exome

AF:

0.421

Gnomad4 FIN exome

AF:

0.348

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.306

AC:

46514

AN:

151964

Hom.:

7873

Cov.:

AF XY:

0.315

AC XY:

23365

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.228

Gnomad4 AMR

AF:

0.371

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.673

Gnomad4 SAS

AF:

0.456

Gnomad4 FIN

AF:

0.364

Gnomad4 NFE

AF:

0.296

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.295

Hom.:

7929

Bravo

AF:

0.305

Asia WGS

AF:

0.560

AC:

1946

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 02, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.11

CADD

Benign

0.15

DANN

Benign

0.20

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over