Variant rs7513351 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024897.4(PAQR6):c.787G>A(p.Glu263Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,603,656 control chromosomes in the GnomAD database, including 25,552 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2461 hom., cov: 33)

Exomes 𝑓: 0.17 ( 23091 hom. )

Consequence

PAQR6
NM_024897.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.812

Variant links:

Genes affected

PAQR6 (HGNC:30132): (progestin and adipoQ receptor family member 6) Predicted to enable signaling receptor activity. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

PAQR6 links:

PAQR6 (HGNC:):

PAQR6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004408896).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAQR6	NM_198406.3 linkuse as main transcript	c.1034G>A	p.Ter345Ter	stop_retained_variant	8/8	ENST00000292291.10	NP_940798.1	Q6TCH4-1Q5TCK7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAQR6	ENST00000292291.10 linkuse as main transcript	c.1034G>A	p.Ter345Ter	stop_retained_variant	8/8	1	NM_198406.3	ENSP00000292291.5		Q6TCH4-1

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26220

AN:

152116

Hom.:

2444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.0805

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.181

GnomAD3 exomes

AF:

0.196

AC:

48606

AN:

247640

Hom.:

5403

AF XY:

0.195

AC XY:

26125

AN XY:

133664

show subpopulations

Gnomad AFR exome

AF:

0.158

Gnomad AMR exome

AF:

0.315

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.243

Gnomad SAS exome

AF:

0.253

Gnomad FIN exome

AF:

0.0806

Gnomad NFE exome

AF:

0.163

Gnomad OTH exome

AF:

0.186

GnomAD4 exome

AF:

0.171

AC:

248843

AN:

1451422

Hom.:

23091

Cov.:

AF XY:

0.174

AC XY:

125048

AN XY:

720144

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.312

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.264

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.0817

Gnomad4 NFE exome

AF:

0.159

Gnomad4 OTH exome

AF:

0.179

GnomAD4 genome

AF:

0.173

AC:

26267

AN:

152234

Hom.:

2461

Cov.:

AF XY:

0.174

AC XY:

12982

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.264

Gnomad4 ASJ

AF:

0.231

Gnomad4 EAS

AF:

0.246

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.0805

Gnomad4 NFE

AF:

0.160

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.167

Hom.:

1102

Bravo

AF:

0.185

TwinsUK

AF:

0.163

AC:

603

ALSPAC

AF:

0.156

AC:

602

ESP6500AA

AF:

0.158

AC:

698

ESP6500EA

AF:

0.164

AC:

1413

ExAC

AF:

0.190

AC:

23117

Asia WGS

AF:

0.271

AC:

940

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.60

CADD

Benign

8.5

DANN

Benign

0.97

DEOGEN2

Benign

0.065

.;.;T;T;T

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.29

LIST_S2

Benign

0.57

T;T;.;.;T

MetaRNN

Benign

0.0044

T;T;T;T;T

MetaSVM

Benign

-0.98

PROVEAN

Benign

0.0

N;.;.;.;.

REVEL

Benign

0.027

Sift

Pathogenic

0.0

D;.;.;.;.

Sift4G

Pathogenic

0.0

D;D;.;.;.

Polyphen

0.0060

B;B;B;B;B

Vest4

0.11

MPC

0.27

ClinPred

0.059

GERP RS

-3.6

gMVP

0.15

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over