chr15-69304102-A-G

Variant names:

• chr15-69304102-A-G
• rs10851802
• NM_017705.4:c.-277+5046A>G

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+5046A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,946 control chromosomes in the GnomAD database, including 35,711 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 0.68 (35711 hom., cov: 30)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.795
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017705.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR5	NM_017705.4	MANE Select	c.-277+5046A>G		intron	N/A	NP_060175.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR5	ENST00000395407.7	TSL:1 MANE Select	c.-277+5046A>G		intron	N/A	ENSP00000378803.2
	PAQR5	ENST00000909133.1		c.-355-501A>G		intron	N/A	ENSP00000579192.1
	PAQR5	ENST00000934600.1		c.-116+5046A>G		intron	N/A	ENSP00000604659.1

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103696 AN: 151828 Hom.: 35695 Cov.: 30

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.683 AC: 103754 AN: 151946 Hom.: 35711 Cov.: 30 AF XY: 0.679 AC XY: 50446 AN XY: 74252

African (AFR) AF: 0.590 AC: 24437 AN: 41406

American (AMR) AF: 0.721 AC: 11014 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2546 AN: 3468

East Asian (EAS) AF: 0.674 AC: 3466 AN: 5142

South Asian (SAS) AF: 0.677 AC: 3265 AN: 4820

European-Finnish (FIN) AF: 0.679 AC: 7150 AN: 10530

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49487 AN: 67986

Other (OTH) AF: 0.707 AC: 1491 AN: 2110

Alfa AF: 0.709 Hom.: 4784

Bravo AF: 0.683

Asia WGS AF: 0.695 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.5
DANN	Benign	0.84
PhyloP100		0.80
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: rs10851802; hg19: chr15-69596441;