7-47796216-G-A

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.8194-66C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,326,426 control chromosomes in the GnomAD database, including 157,595 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (15403 hom., cov: 33)
  • Exomes 𝑓: 0.49 (142192 hom.)
• Consequence: PKD1L1 NM_138295.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.731

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=-0.93).
• BP6: Variant 7-47796216-G-A is Benign according to our data. Variant chr7-47796216-G-A is described in ClinVar as [Benign]. Clinvar id is 1276259.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKD1L1	NM_138295.5	c.8194-66C>T		intron_variant		ENST00000289672.7
PKD1L1-AS1	NR_161269.1	n.153+773G>A		intron_variant, non_coding_transcript_variant
PKD1L1	XM_017011798.3	c.8371-66C>T		intron_variant
PKD1L1-AS1	NR_161268.1	n.153+773G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKD1L1	ENST00000289672.7	c.8194-66C>T		intron_variant		1	NM_138295.5	P2
PKD1L1-AS1	ENST00000623971.3	n.153+773G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66936 AN: 151854 Hom.: 15399 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.474

GnomAD4 exome AF: 0.490 AC: 575927 AN: 1174454 Hom.: 142192 AF XY: 0.490 AC XY: 287889 AN XY: 587984

Gnomad4 AFR exome AF: 0.300

Gnomad4 AMR exome AF: 0.476

Gnomad4 ASJ exome AF: 0.459

Gnomad4 EAS exome AF: 0.590

Gnomad4 SAS exome AF: 0.434

Gnomad4 FIN exome AF: 0.412

Gnomad4 NFE exome AF: 0.501

Gnomad4 OTH exome AF: 0.482

GnomAD4 genome AF: 0.440 AC: 66943 AN: 151972 Hom.: 15403 Cov.: 33 AF XY: 0.438 AC XY: 32515 AN XY: 74284

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.478

Alfa AF: 0.456 Hom.: 3167

Bravo AF: 0.440

Asia WGS AF: 0.492 AC: 1709 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

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.46
Dann	Benign	0.66

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: rs6943728; hg19: chr7-47835814; COSMIC: COSV51842711;