chr15-69304869-A-G

Variant names:

• chr15-69304869-A-G
• rs12441411
• NM_017705.4:c.-277+5813A>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+5813A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 152,298 control chromosomes in the GnomAD database, including 177 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 0.040 (177 hom., cov: 32)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAQR5	NM_017705.4	c.-277+5813A>G		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+5813A>G		intron_variant	Intron 1 of 8	1	NM_017705.4	ENSP00000378803.2
PAQR5	ENST00000558684.5	c.-243+5813A>G		intron_variant	Intron 1 of 4	5		ENSP00000453009.1

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6063 AN: 152180 Hom.: 176 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0206

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0398 AC: 6069 AN: 152298 Hom.: 177 Cov.: 32 AF XY: 0.0413 AC XY: 3077 AN XY: 74456

African (AFR) AF: 0.0509 AC: 2117 AN: 41570

American (AMR) AF: 0.0597 AC: 913 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3470

East Asian (EAS) AF: 0.127 AC: 659 AN: 5180

South Asian (SAS) AF: 0.0375 AC: 181 AN: 4828

European-Finnish (FIN) AF: 0.0541 AC: 574 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0206 AC: 1403 AN: 68032

Other (OTH) AF: 0.0436 AC: 92 AN: 2110

Alfa AF: 0.0360 Hom.: 80

Bravo AF: 0.0433

Asia WGS AF: 0.0990 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.17
DANN	Benign	0.77
PhyloP100		-1.6
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: rs12441411; hg19: chr15-69597208;