rs7800244

chr7-47740371-G-T

Variant summary

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

The ENST00000648482.1(PKD1L1):c.*393C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,898 control chromosomes in the GnomAD database, including 1,968 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 0.15 (1968 hom., cov: 32)
• Consequence: PKD1L1 ENST00000648482.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

Genes affected

PKD1L1 (HGNC:18053): (polycystin 1 like 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family containing 11 transmembrane domains, a receptor for egg jelly (REJ) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. The encoded protein may play a role in the male reproductive system. Alternative splice variants have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKD1L1	ENST00000648482.1	c.*393C>A		3_prime_UTR_variant	8/8

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22865 AN: 151788 Hom.: 1967 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.151 AC: 22872 AN: 151898 Hom.: 1968 Cov.: 32 AF XY: 0.154 AC XY: 11396 AN XY: 74238

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.144

Alfa AF: 0.171 Hom.: 3087

Bravo AF: 0.143

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.9
Dann	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7800244; hg19: chr7-47779969;