16-81189691-C-T

Position:

• chr16-81189691-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000525539.5(PKD1L2):​c.1672-693G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,106 control chromosomes in the GnomAD database, including 2,144 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 0.16 (2144 hom., cov: 32)
• Consequence: PKD1L2 ENST00000525539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKD1L2	NR_126532.3	n.1687-693G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD1L2	ENST00000525539.5	c.1672-693G>A		intron_variant		1		ENSP00000434417.1
PKD1L2	ENST00000526632.5	c.253-693G>A		intron_variant		2		ENSP00000436389.1
PKD1L2	ENST00000710634.1	n.285+974G>A		intron_variant				ENSP00000518389.1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24629 AN: 151988 Hom.: 2137 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.161

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.162 AC: 24656 AN: 152106 Hom.: 2144 Cov.: 32 AF XY: 0.161 AC XY: 11975 AN XY: 74378

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0830 Hom.: 132

Bravo AF: 0.159

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.081
DANN	Benign	0.83

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

Other links and lift over

dbSNP: rs9931907; hg19: chr16-81223296;