rs11072089

Variant names:

• chr15-69357714-C-T
• rs11072089
• NM_017705.4:c.-115-2252C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PAQR5	NM_017705.4	c.-115-2252C>T		intron_variant	Intron 2 of 8	ENST00000395407.7	NP_060175.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAQR5	ENST00000395407.7	c.-115-2252C>T		intron_variant	Intron 2 of 8	1	NM_017705.4	ENSP00000378803.2
PAQR5	ENST00000561153.5	c.-115-2252C>T		intron_variant	Intron 2 of 8	5		ENSP00000453526.1
PAQR5	ENST00000558684.5	c.-82+20213C>T		intron_variant	Intron 2 of 4	5		ENSP00000453009.1

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

African (AFR) AF: 0.505 AC: 20934 AN: 41416

American (AMR) AF: 0.811 AC: 12383 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3322 AN: 3472

East Asian (EAS) AF: 0.727 AC: 3765 AN: 5178

South Asian (SAS) AF: 0.940 AC: 4530 AN: 4818

European-Finnish (FIN) AF: 0.889 AC: 9429 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65322 AN: 68032

Other (OTH) AF: 0.845 AC: 1785 AN: 2112

Alfa AF: 0.893 Hom.: 104292

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
PhyloP100		0.047
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11072089; hg19: chr15-69650053;