chr16-81189691-C-T

Variant names:

• chr16-81189691-C-T
• rs9931907
• ENST00000525539.5:c.1672-693G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525539.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD1L2	NR_126532.3		n.1687-693G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD1L2	ENST00000525539.5	TSL:1	c.1672-693G>A		intron	N/A	ENSP00000434417.1
	PKD1L2	ENST00000526632.5	TSL:2	c.253-693G>A		intron	N/A	ENSP00000436389.1
	PKD1L2	ENST00000710634.1		n.285+974G>A		intron	N/A	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

African (AFR) AF: 0.174 AC: 7227 AN: 41464

American (AMR) AF: 0.176 AC: 2681 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3468

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5174

South Asian (SAS) AF: 0.246 AC: 1190 AN: 4830

European-Finnish (FIN) AF: 0.137 AC: 1448 AN: 10582

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10771 AN: 68002

Other (OTH) AF: 0.162 AC: 341 AN: 2110

Alfa AF: 0.0857 Hom.: 142

Bravo AF: 0.159

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.081
DANN	Benign	0.83
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9931907; hg19: chr16-81223296;