Genetic Variant PAQR5:c.*88T>C (chr15-69403910-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_017705.4(PAQR5):c.*88T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 1,396,354 control chromosomes in the GnomAD database, including 618,142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.84 ( 56167 hom., cov: 32)

Exomes 𝑓: 0.95 ( 561975 hom. )

Consequence

PAQR5
NM_017705.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219

Variant links:

Genes affected

PAQR5 (HGNC:29645): (progestin and adipoQ receptor family member 5) Predicted to enable signaling receptor activity. Predicted to be involved in oogenesis. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

PAQR5 links:

KIF23-AS1 (HGNC:27075): (KIF23 and PAQR5 antisense RNA 1)

KIF23-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAQR5	NM_017705.4 link	c.*88T>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000395407.7	NP_060175.3	Q9NXK6A0A024R607

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAQR5	ENST00000395407.7 link	c.*88T>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_017705.4	ENSP00000378803.2		Q9NXK6

Frequencies

GnomAD3 genomes

AF:

0.845

AC:

128400

AN:

152024

Hom.:

56156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.976

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.964

Gnomad EAS

AF:

0.705

Gnomad SAS

AF:

0.950

Gnomad FIN

AF:

0.923

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.972

Gnomad OTH

AF:

0.875

GnomAD4 exome

AF:

0.947

AC:

1178490

AN:

1244210

Hom.:

561975

Cov.:

AF XY:

0.949

AC XY:

588211

AN XY:

619698

show subpopulations

Gnomad4 AFR exome

AF:

0.617

Gnomad4 AMR exome

AF:

0.754

Gnomad4 ASJ exome

AF:

0.971

Gnomad4 EAS exome

AF:

0.705

Gnomad4 SAS exome

AF:

0.958

Gnomad4 FIN exome

AF:

0.933

Gnomad4 NFE exome

AF:

0.974

Gnomad4 OTH exome

AF:

0.929

GnomAD4 genome

AF:

0.844

AC:

128447

AN:

152144

Hom.:

56167

Cov.:

AF XY:

0.842

AC XY:

62625

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.612

Gnomad4 AMR

AF:

0.826

Gnomad4 ASJ

AF:

0.964

Gnomad4 EAS

AF:

0.705

Gnomad4 SAS

AF:

0.949

Gnomad4 FIN

AF:

0.923

Gnomad4 NFE

AF:

0.972

Gnomad4 OTH

AF:

0.876

Alfa

AF:

0.952

Hom.:

135151

Bravo

AF:

0.824

Asia WGS

AF:

0.810

AC:

2817

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.3

DANN

Benign

0.57

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