rs11072089

Positions:

• chr15-69357714-C-T

Variant summary

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

The NM_017705.4(PAQR5):​c.-115-2252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,118 control chromosomes in the GnomAD database, including 52,347 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 0.81 (52347 hom., cov: 33)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAQR5	NM_017705.4	c.-115-2252C>T		intron_variant		ENST00000395407.7	NP_060175.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAQR5	ENST00000395407.7	c.-115-2252C>T		intron_variant		1	NM_017705.4	ENSP00000378803	P1
PAQR5	ENST00000558684.5	c.-82+20213C>T		intron_variant		5		ENSP00000453009
PAQR5	ENST00000561153.5	c.-115-2252C>T		intron_variant		5		ENSP00000453526	P1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122537 AN: 152000 Hom.: 52335 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.844

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.806 AC: 122578 AN: 152118 Hom.: 52347 Cov.: 33 AF XY: 0.804 AC XY: 59839 AN XY: 74390

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.957

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.845

Alfa AF: 0.911 Hom.: 22729

Bravo AF: 0.782

Asia WGS AF: 0.808 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.40

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: rs11072089; hg19: chr15-69650053;