rs12670472

Positions:

• chr7-47771532-T-A
• chr7-47771532-T-C

Variant summary

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

The ENST00000648482.1(PKD1L1):​c.1159+21095A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,206 control chromosomes in the GnomAD database, including 3,446 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 0.19 (3446 hom., cov: 33)
• Consequence: PKD1L1 ENST00000648482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 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.1159+21095A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29325 AN: 152088 Hom.: 3442 Cov.: 33

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.193 AC: 29333 AN: 152206 Hom.: 3446 Cov.: 33 AF XY: 0.191 AC XY: 14217 AN XY: 74418

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.208

Alfa AF: 0.119 Hom.: 217

Bravo AF: 0.190

Asia WGS AF: 0.233 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12670472; hg19: chr7-47811130;