rs1453282

Variant names:

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

Variant summary

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

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]

PKD1L1 Gene-Disease associations (from GenCC):

• heterotaxy, visceral, 8, autosomal

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• situs inversus

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648482.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKD1L1	ENST00000648482.1		c.1159-8573A>G		intron	N/A	ENSP00000496786.1	A0A3B3IRH7

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

African (AFR) AF: 0.766 AC: 31773 AN: 41454

American (AMR) AF: 0.539 AC: 8245 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1780 AN: 5180

South Asian (SAS) AF: 0.515 AC: 2474 AN: 4808

European-Finnish (FIN) AF: 0.631 AC: 6668 AN: 10570

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40262 AN: 67978

Other (OTH) AF: 0.588 AC: 1238 AN: 2104

Alfa AF: 0.601 Hom.: 11909

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.77
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs1453282; hg19: chr7-47789084;