rs1453282

Variant names:

• chr7-47749486-T-C
• rs1453282
• ENST00000648482.1:c.1159-8573A>G

Variant summary

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

The ENST00000648482.1(PKD1L1):​c.1159-8573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,060 control chromosomes in the GnomAD database, including 30,479 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 0.62 (30479 hom., cov: 32)
• Consequence: PKD1L1 ENST00000648482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKD1L1	ENST00000648482.1	c.1159-8573A>G		intron_variant	Intron 7 of 7			ENSP00000496786.1

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94758 AN: 151942 Hom.: 30436 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.624 AC: 94850 AN: 152060 Hom.: 30479 Cov.: 32 AF XY: 0.620 AC XY: 46082 AN XY: 74308

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.588

Alfa AF: 0.599 Hom.: 9736

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1453282; hg19: chr7-47789084;