15-69336545-C-T

Variant names:

• chr15-69336545-C-T
• rs4505253
• NM_017705.4:c.-276-796C>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.-276-796C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,022 control chromosomes in the GnomAD database, including 34,029 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 0.65 (34029 hom., cov: 33)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAQR5	NM_017705.4	c.-276-796C>T		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.-276-796C>T		intron_variant	Intron 1 of 8	1	NM_017705.4	ENSP00000378803.2
PAQR5	ENST00000561153.5	c.-280-796C>T		intron_variant	Intron 1 of 8	5		ENSP00000453526.1
PAQR5	ENST00000558684.5	c.-242-796C>T		intron_variant	Intron 1 of 4	5		ENSP00000453009.1

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98424 AN: 151904 Hom.: 34023 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.648 AC: 98444 AN: 152022 Hom.: 34029 Cov.: 33 AF XY: 0.648 AC XY: 48126 AN XY: 74300

African (AFR) AF: 0.389 AC: 16115 AN: 41438

American (AMR) AF: 0.675 AC: 10324 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2619 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3159 AN: 5178

South Asian (SAS) AF: 0.830 AC: 4004 AN: 4826

European-Finnish (FIN) AF: 0.713 AC: 7524 AN: 10546

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52353 AN: 67964

Other (OTH) AF: 0.685 AC: 1443 AN: 2108

Alfa AF: 0.698 Hom.: 4579

Bravo AF: 0.627

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.70
DANN	Benign	0.86
PhyloP100		-1.3
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: rs4505253; hg19: chr15-69628884;