chr15-69305787-T-A

Variant names:

• chr15-69305787-T-A
• rs7173953
• NM_017705.4:c.-277+6731T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017705.4(PAQR5):​c.-277+6731T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,922 control chromosomes in the GnomAD database, including 29,367 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 0.62 (29367 hom., cov: 31)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656
• Publications: 3 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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAQR5	NM_017705.4	c.-277+6731T>A		intron_variant	Intron 1 of 8	ENST00000395407.7	NP_060175.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAQR5	ENST00000395407.7	c.-277+6731T>A		intron_variant	Intron 1 of 8	1	NM_017705.4	ENSP00000378803.2
PAQR5	ENST00000558684.5	c.-243+6731T>A		intron_variant	Intron 1 of 4	5		ENSP00000453009.1

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93706 AN: 151804 Hom.: 29367 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.617 AC: 93737 AN: 151922 Hom.: 29367 Cov.: 31 AF XY: 0.613 AC XY: 45520 AN XY: 74240

African (AFR) AF: 0.525 AC: 21754 AN: 41418

American (AMR) AF: 0.570 AC: 8705 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2414 AN: 5142

South Asian (SAS) AF: 0.500 AC: 2402 AN: 4804

European-Finnish (FIN) AF: 0.681 AC: 7182 AN: 10542

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.690 AC: 46895 AN: 67950

Other (OTH) AF: 0.633 AC: 1337 AN: 2112

Alfa AF: 0.547 Hom.: 1588

Bravo AF: 0.606

Asia WGS AF: 0.492 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	19
DANN	Benign	0.88
PhyloP100		0.66
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: rs7173953; hg19: chr15-69598126;