rs17112901

chr10-100306428-C-T

Variant summary

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

The NM_016112.3(PKD2L1):c.350-6710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,110 control chromosomes in the GnomAD database, including 2,659 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 0.17 (2659 hom., cov: 31)
• Consequence: PKD2L1 NM_016112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKD2L1	NM_016112.3	c.350-6710G>A		intron_variant		ENST00000318222.4
PKD2L1	NM_001253837.2	c.209-6710G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKD2L1	ENST00000318222.4	c.350-6710G>A		intron_variant		1	NM_016112.3	P1
PKD2L1	ENST00000528248.1	c.*90-6710G>A		intron_variant, NMD_transcript_variant		1
PKD2L1	ENST00000465680.2	c.105-17950G>A		intron_variant		3
PKD2L1	ENST00000532547.1	c.*94-6710G>A		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26027 AN: 151988 Hom.: 2657 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.171 AC: 26062 AN: 152110 Hom.: 2659 Cov.: 31 AF XY: 0.171 AC XY: 12734 AN XY: 74382

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.152

Alfa AF: 0.127 Hom.: 1338

Bravo AF: 0.175

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.35

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: rs17112901; hg19: chr10-102066185;