Variant 10-100329906-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001253837.2(PKD2L1):c.35G>A(p.Cys12Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,612,588 control chromosomes in the GnomAD database, including 16,645 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 0.12 ( 1326 hom., cov: 32)

Exomes 𝑓: 0.13 ( 15319 hom. )

Consequence

PKD2L1
NM_001253837.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.224

Variant links:

Genes affected

PKD2L1 (HGNC:9011): (polycystin 2 like 1, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein contains multiple transmembrane domains, and cytoplasmic N- and C-termini. The protein may be an integral membrane protein involved in cell-cell/matrix interactions. This protein functions as a calcium-regulated nonselective cation channel. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

PKD2L1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKD2L1	NM_016112.3 linkuse as main transcript	c.198G>A	p.Val66Val	synonymous_variant	1/16	ENST00000318222.4	NP_057196.2	Q9P0L9-1
PKD2L1	NM_001253837.2 linkuse as main transcript	c.35G>A	p.Cys12Tyr	missense_variant	1/16		NP_001240766.1	Q9P0L9Q1L4F0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PKD2L1	ENST00000318222.4 linkuse as main transcript	c.198G>A	p.Val66Val	synonymous_variant	1/16	1	NM_016112.3	ENSP00000325296.3	Q9P0L9-1
PKD2L1	ENST00000528248.1 linkuse as main transcript	n.33G>A		non_coding_transcript_exon_variant	1/16	1		ENSP00000436514.1	H0YET4
PKD2L1	ENST00000465680.2 linkuse as main transcript	c.66G>A	p.Val22Val	synonymous_variant	1/2	3		ENSP00000434019.1	H0YDN7
PKD2L1	ENST00000532547.1 linkuse as main transcript	n.195+3G>A		splice_region_variant, intron_variant		4		ENSP00000434224.1	E9PRD1

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18588

AN:

152100

Hom.:

1323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.0339

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.128

GnomAD3 exomes

AF:

0.138

AC:

34715

AN:

250700

Hom.:

3214

AF XY:

0.151

AC XY:

20456

AN XY:

135494

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.0663

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.0356

Gnomad SAS exome

AF:

0.313

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.142

GnomAD4 exome

AF:

0.135

AC:

196529

AN:

1460370

Hom.:

15319

Cov.:

AF XY:

0.141

AC XY:

102351

AN XY:

726514

show subpopulations

Gnomad4 AFR exome

AF:

0.105

Gnomad4 AMR exome

AF:

0.0712

Gnomad4 ASJ exome

AF:

0.196

Gnomad4 EAS exome

AF:

0.0263

Gnomad4 SAS exome

AF:

0.306

Gnomad4 FIN exome

AF:

0.107

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.122

AC:

18603

AN:

152218

Hom.:

1326

Cov.:

AF XY:

0.123

AC XY:

9172

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.104

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.180

Gnomad4 EAS

AF:

0.0340

Gnomad4 SAS

AF:

0.301

Gnomad4 FIN

AF:

0.105

Gnomad4 NFE

AF:

0.130

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.130

Hom.:

752

Bravo

AF:

0.118

Asia WGS

AF:

0.196

AC:

682

AN:

3478

EpiCase

AF:

0.138

EpiControl

AF:

0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.59

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.59

Position offset: 3

DS_DL_spliceai

0.25

Position offset: -37

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