Variant chr7-47833247-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_138295.5(PKD1L1):c.6180T>C(p.Pro2060Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 1,611,464 control chromosomes in the GnomAD database, including 430,176 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 39308 hom., cov: 33)

Exomes 𝑓: 0.73 ( 390868 hom. )

Consequence

PKD1L1
NM_138295.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.922

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 7-47833247-A-G is Benign according to our data. Variant chr7-47833247-A-G is described in ClinVar as [Benign]. Clinvar id is 1234377.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.922 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKD1L1	NM_138295.5 linkuse as main transcript	c.6180T>C	p.Pro2060Pro	synonymous_variant	41/57	ENST00000289672.7	NP_612152.1
PKD1L1	XM_017011798.3 linkuse as main transcript	c.6357T>C	p.Pro2119Pro	synonymous_variant	42/59		XP_016867287.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PKD1L1	ENST00000289672.7 linkuse as main transcript	c.6180T>C	p.Pro2060Pro	synonymous_variant	41/57	1	NM_138295.5	ENSP00000289672.2	Q8TDX9-1
PKD1L1	ENST00000690269.1 linkuse as main transcript	c.6180T>C	p.Pro2060Pro	synonymous_variant	41/58			ENSP00000510743.1	A0A8I5KWV8
PKD1L1	ENST00000685709.1 linkuse as main transcript	c.6012T>C	p.Pro2004Pro	synonymous_variant	40/56			ENSP00000509540.1	A0A8I5QKU1
PKD1L1	ENST00000686775.1 linkuse as main transcript	c.375+1092T>C		intron_variant				ENSP00000508550.1	A0A8I5KS31

Frequencies

GnomAD3 genomes

AF:

0.717

AC:

109062

AN:

152038

Hom.:

39277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.799

Gnomad AMR

AF:

0.744

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.889

Gnomad SAS

AF:

0.654

Gnomad FIN

AF:

0.690

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.738

Gnomad OTH

AF:

0.709

GnomAD3 exomes

AF:

0.732

AC:

181195

AN:

247468

Hom.:

66721

AF XY:

0.726

AC XY:

97041

AN XY:

133588

show subpopulations

Gnomad AFR exome

AF:

0.668

Gnomad AMR exome

AF:

0.764

Gnomad ASJ exome

AF:

0.722

Gnomad EAS exome

AF:

0.893

Gnomad SAS exome

AF:

0.651

Gnomad FIN exome

AF:

0.686

Gnomad NFE exome

AF:

0.737

Gnomad OTH exome

AF:

0.727

GnomAD4 exome

AF:

0.731

AC:

1066575

AN:

1459308

Hom.:

390868

Cov.:

AF XY:

0.729

AC XY:

529024

AN XY:

725660

show subpopulations

Gnomad4 AFR exome

AF:

0.663

Gnomad4 AMR exome

AF:

0.759

Gnomad4 ASJ exome

AF:

0.721

Gnomad4 EAS exome

AF:

0.893

Gnomad4 SAS exome

AF:

0.649

Gnomad4 FIN exome

AF:

0.687

Gnomad4 NFE exome

AF:

0.735

Gnomad4 OTH exome

AF:

0.734

GnomAD4 genome

AF:

0.717

AC:

109146

AN:

152156

Hom.:

39308

Cov.:

AF XY:

0.718

AC XY:

53412

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.665

Gnomad4 AMR

AF:

0.743

Gnomad4 ASJ

AF:

0.714

Gnomad4 EAS

AF:

0.889

Gnomad4 SAS

AF:

0.655

Gnomad4 FIN

AF:

0.690

Gnomad4 NFE

AF:

0.738

Gnomad4 OTH

AF:

0.711

Alfa

AF:

0.732

Hom.:

67387

Bravo

AF:

0.721

Asia WGS

AF:

0.760

AC:

2640

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Heterotaxy, visceral, 8, autosomal

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.35

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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