rs921630

Positions:

• chr7-47755460-A-G

Variant summary

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

The ENST00000648482.1(PKD1L1):​c.1160-14547T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,972 control chromosomes in the GnomAD database, including 17,035 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 0.47 (17035 hom., cov: 32)
• Consequence: PKD1L1 ENST00000648482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKD1L1	ENST00000648482.1	c.1160-14547T>C		intron_variant				ENSP00000496786

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71196 AN: 151854 Hom.: 17022 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.469 AC: 71247 AN: 151972 Hom.: 17035 Cov.: 32 AF XY: 0.471 AC XY: 35000 AN XY: 74280

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.474

Alfa AF: 0.475 Hom.: 29209

Bravo AF: 0.471

Asia WGS AF: 0.522 AC: 1815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921630; hg19: chr7-47795058;