rs7172559

Positions:

• chr15-69385159-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.385+277C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 152,308 control chromosomes in the GnomAD database, including 73 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 0.018 (73 hom., cov: 32)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAQR5	NM_017705.4	c.385+277C>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.385+277C>T		intron_variant		1	NM_017705.4	ENSP00000378803	P1

Frequencies

GnomAD3 genomes AF: 0.0182 AC: 2771 AN: 152190 Hom.: 73 Cov.: 32

Gnomad AFR AF: 0.00772

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00863

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0182 AC: 2771 AN: 152308 Hom.: 73 Cov.: 32 AF XY: 0.0199 AC XY: 1479 AN XY: 74472

Gnomad4 AFR AF: 0.00770

Gnomad4 AMR AF: 0.0474

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0335

Gnomad4 NFE AF: 0.00863

Gnomad4 OTH AF: 0.0204

Alfa AF: 0.0221 Hom.: 17

Bravo AF: 0.0220

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.57

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: rs7172559; hg19: chr15-69677498;