Genetic Variant PKD1L1:c.8193+163G>A (chr7-47800486-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.158

Publications

5 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138295.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PKD1L1	NM_138295.5	MANE Select	c.8193+163G>A	intron	N/A	NP_612152.1	Q8TDX9-1
PKD1L1-AS1	NR_161268.1		n.153+5043C>T	intron	N/A
PKD1L1-AS1	NR_161269.1		n.153+5043C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PKD1L1	ENST00000289672.7	TSL:1 MANE Select	c.8193+163G>A	intron	N/A	ENSP00000289672.2	Q8TDX9-1
PKD1L1-AS1	ENST00000623971.3	TSL:1	n.153+5043C>T	intron	N/A
PKD1L1	ENST00000690269.1		c.8193+163G>A	intron	N/A	ENSP00000510743.1	A0A8I5KWV8

Frequencies

GnomAD3 genomes

AF:

0.0564

AC:

8586

AN:

152104

Hom.:

375

Cov.:

show subpopulations

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.:

AF XY:

0.0564

AC XY:

4195

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0163

AC:

678

AN:

41540

American (AMR)

AF:

0.0863

AC:

1321

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0214

AC:

AN:

3466

East Asian (EAS)

AF:

0.198

AC:

1026

AN:

5178

South Asian (SAS)

AF:

0.0491

AC:

237

AN:

4826

European-Finnish (FIN)

AF:

0.0559

AC:

592

AN:

10596

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0656

AC:

4461

AN:

67998

Other (OTH)

AF:

0.0502

AC:

106

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

406

812

1217

1623

2029

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0569

Hom.:

Bravo

AF:

0.0590

Asia WGS

AF:

0.128

AC:

445

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.8

(source)

DANN

Benign

0.62

PhyloP100

0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over