rs4724620

Positions:

• chr7-47751314-T-C

Variant summary

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

The ENST00000648482.1(PKD1L1):​c.1160-10401A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,090 control chromosomes in the GnomAD database, including 59,430 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 0.88 (59430 hom., cov: 30)
• Consequence: PKD1L1 ENST00000648482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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 = 0.955 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.1160-10401A>G		intron_variant				ENSP00000496786

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134214 AN: 151972 Hom.: 59379 Cov.: 30

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.883 AC: 134322 AN: 152090 Hom.: 59430 Cov.: 30 AF XY: 0.887 AC XY: 65939 AN XY: 74312

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.876

Alfa AF: 0.873 Hom.: 79915

Bravo AF: 0.883

Asia WGS AF: 0.932 AC: 3241 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	0.37
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4724620; hg19: chr7-47790912;