1-156243466-G-A

Position:

• chr1-156243466-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198406.3(PAQR6):​c.*663C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 460,080 control chromosomes in the GnomAD database, including 126,266 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency:
  • Genomes: 𝑓 0.75 (42878 hom., cov: 31)
  • Exomes 𝑓: 0.73 (83388 hom.)
• Consequence: PAQR6 NM_198406.3 3_prime_UTR
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.382

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAQR6	NM_198406.3	c.*663C>T		3_prime_UTR_variant	8/8	ENST00000292291.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAQR6	ENST00000292291.10	c.*663C>T		3_prime_UTR_variant	8/8	1	NM_198406.3	P4

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113606 AN: 151846 Hom.: 42825 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.753

GnomAD4 exome AF: 0.732 AC: 225525 AN: 308116 Hom.: 83388 Cov.: 5 AF XY: 0.734 AC XY: 116160 AN XY: 158180

Gnomad4 AFR exome AF: 0.803

Gnomad4 AMR exome AF: 0.841

Gnomad4 ASJ exome AF: 0.785

Gnomad4 EAS exome AF: 0.736

Gnomad4 SAS exome AF: 0.777

Gnomad4 FIN exome AF: 0.567

Gnomad4 NFE exome AF: 0.727

Gnomad4 OTH exome AF: 0.736

GnomAD4 genome AF: 0.748 AC: 113719 AN: 151964 Hom.: 42878 Cov.: 31 AF XY: 0.743 AC XY: 55200 AN XY: 74250

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.755

Alfa AF: 0.745 Hom.: 43603

Bravo AF: 0.771

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Nephrolithiasis, calcium oxalate Other:1

association, no assertion criteria provided

case-control

Division of Molecular Genetics and Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University

Mar 01, 2014

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.30

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

Other links and lift over

dbSNP: rs759330; hg19: chr1-156213257;