7-47800486-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_138295.5(PKD1L1):c.8193+163G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,222 control chromosomes in the GnomAD database, including 377 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.056 (377 hom., cov: 32)
• Consequence: PKD1L1 NM_138295.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.158

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-AS1 (HGNC:21911): (PKD1L1 antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 7-47800486-C-T is Benign according to our data. Variant chr7-47800486-C-T is described in ClinVar as [Benign]. Clinvar id is 1243978.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKD1L1	NM_138295.5	c.8193+163G>A		intron_variant		ENST00000289672.7
PKD1L1-AS1	NR_161269.1	n.153+5043C>T		intron_variant, non_coding_transcript_variant
PKD1L1	XM_017011798.3	c.8370+163G>A		intron_variant
PKD1L1-AS1	NR_161268.1	n.153+5043C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKD1L1	ENST00000289672.7	c.8193+163G>A		intron_variant		1	NM_138295.5	P2
PKD1L1-AS1	ENST00000623971.3	n.153+5043C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8586 AN: 152104 Hom.: 375 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0214

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0565 AC: 8595 AN: 152222 Hom.: 377 Cov.: 32 AF XY: 0.0564 AC XY: 4195 AN XY: 74422

Gnomad4 AFR AF: 0.0163

Gnomad4 AMR AF: 0.0863

Gnomad4 ASJ AF: 0.0214

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0586 Hom.: 32

Bravo AF: 0.0590

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.8
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734933; hg19: chr7-47840084;