rs9381994

Positions:

chr6-51619163-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_138694.4(PKHD1):c.12143A>G(p.Gln4048Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 1,613,906 control chromosomes in the GnomAD database, including 248,948 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 21709 hom., cov: 35)

Exomes 𝑓: 0.56 ( 227239 hom. )

Consequence

PKHD1
NM_138694.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 0.422

Variant links:

Genes affected

PKHD1 (HGNC:9016): (PKHD1 ciliary IPT domain containing fibrocystin/polyductin) The protein encoded by this gene is predicted to have a single transmembrane (TM)-spanning domain and multiple copies of an immunoglobulin-like plexin-transcription-factor domain. Alternative splicing results in two transcript variants encoding different isoforms. Other alternatively spliced transcripts have been described, but the full length sequences have not been determined. Several of these transcripts are predicted to encode truncated products which lack the TM and may be secreted. Mutations in this gene cause autosomal recessive polycystic kidney disease, also known as polycystic kidney and hepatic disease-1. [provided by RefSeq, Jul 2008]

PKHD1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.0750294E-5).

BP6

Variant 6-51619163-T-C is Benign according to our data. Variant chr6-51619163-T-C is described in ClinVar as [Benign]. Clinvar id is 96376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-51619163-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKHD1	NM_138694.4 linkuse as main transcript	c.12143A>G	p.Gln4048Arg	missense_variant	67/67	ENST00000371117.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKHD1	ENST00000371117.8 linkuse as main transcript	c.12143A>G	p.Gln4048Arg	missense_variant	67/67	1	NM_138694.4	P2	P08F94-1
	ENST00000589278.6 linkuse as main transcript	n.811-3197T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000454361.1 linkuse as main transcript	n.81-3192T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000650088.1 linkuse as main transcript	n.222-3192T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.533

AC:

81013

AN:

152104

Hom.:

21711

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.397

Gnomad AMR

AF:

0.580

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.586

Gnomad SAS

AF:

0.643

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.524

GnomAD3 exomes

AF:

0.566

AC:

142135

AN:

250914

Hom.:

40633

AF XY:

0.566

AC XY:

76708

AN XY:

135618

show subpopulations

Gnomad AFR exome

AF:

0.479

Gnomad AMR exome

AF:

0.650

Gnomad ASJ exome

AF:

0.499

Gnomad EAS exome

AF:

0.585

Gnomad SAS exome

AF:

0.630

Gnomad FIN exome

AF:

0.526

Gnomad NFE exome

AF:

0.548

Gnomad OTH exome

AF:

0.554

GnomAD4 exome

AF:

0.556

AC:

813130

AN:

1461684

Hom.:

227239

Cov.:

AF XY:

0.558

AC XY:

406037

AN XY:

727146

show subpopulations

Gnomad4 AFR exome

AF:

0.475

Gnomad4 AMR exome

AF:

0.637

Gnomad4 ASJ exome

AF:

0.492

Gnomad4 EAS exome

AF:

0.591

Gnomad4 SAS exome

AF:

0.626

Gnomad4 FIN exome

AF:

0.531

Gnomad4 NFE exome

AF:

0.552

Gnomad4 OTH exome

AF:

0.547

GnomAD4 genome

AF:

0.532

AC:

81035

AN:

152222

Hom.:

21709

Cov.:

AF XY:

0.532

AC XY:

39565

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.478

Gnomad4 AMR

AF:

0.580

Gnomad4 ASJ

AF:

0.489

Gnomad4 EAS

AF:

0.587

Gnomad4 SAS

AF:

0.643

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.550

Gnomad4 OTH

AF:

0.522

Alfa

AF:

0.547

Hom.:

56367

Bravo

AF:

0.536

TwinsUK

AF:

0.549

AC:

2035

ALSPAC

AF:

0.551

AC:

2125

ESP6500AA

AF:

0.481

AC:

2120

ESP6500EA

AF:

0.549

AC:

4719

ExAC

AF:

0.563

AC:

68311

Asia WGS

AF:

0.597

AC:

2076

AN:

3476

EpiCase

AF:

0.549

EpiControl

AF:

0.554

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Autosomal recessive polycystic kidney disease

Benign:3

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	May 11, 2017	- -

Polycystic kidney disease 4

Benign:3

Benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 25, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Pars Genome Lab	Jun 19, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 27, 2015	- -

Polycystic kidney disease

Benign:1

Benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

Thec.12143A>G, p.Gln4048Arg variant was identified in 56.3% of 68262 control alleles in the Exome Aggregation Consortium (March 14, 2016). According to ACMG guidelines for variant classification based on allele frequency, category BA1, this variant is considered benign and has not been further reviewed (Richards 2015). -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 29, 2019

This variant is associated with the following publications: (PMID: 28509106) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.16

Eigen

Benign

-0.41

Eigen_PC

Benign

-0.28

FATHMM_MKL

Benign

0.26

LIST_S2

Benign

0.51

MetaRNN

Benign

0.000011

MetaSVM

Benign

-0.83

MutationAssessor

Benign

1.5

MutationTaster

Benign

1.0

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.75

REVEL

Benign

0.21

Sift

Benign

0.52

Sift4G

Benign

0.25

Polyphen

0.031

Vest4

0.021

MPC

0.064

ClinPred

0.010

GERP RS

4.0

Varity_R

0.046

gMVP

0.16

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