Variant 7-47796216-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.731

Variant links:

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 links:

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

PKD1L1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	MANE
PKD1L1	NM_138295.5 linkuse as main transcript	c.8194-66C>T	intron_variant	ENST00000289672.7
PKD1L1-AS1	NR_161269.1 linkuse as main transcript	n.153+773G>A	intron_variant, non_coding_transcript_variant
PKD1L1	XM_017011798.3 linkuse as main transcript	c.8371-66C>T	intron_variant
PKD1L1-AS1	NR_161268.1 linkuse as main transcript	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 linkuse as main transcript	c.8194-66C>T		intron_variant		1	NM_138295.5	P2	Q8TDX9-1
PKD1L1-AS1	ENST00000623971.3 linkuse as main transcript	n.153+773G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

66936

AN:

151854

Hom.:

15399

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.438

AC XY:

32515

AN XY:

74284

show subpopulations

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over