rs12900857

chr15-69356887-C-Achr15-69356887-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017705.4(PAQR5):c.-115-3079C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,060 control chromosomes in the GnomAD database, including 52,789 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 0.81 (52789 hom., cov: 31)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAQR5	NM_017705.4	c.-115-3079C>A		intron_variant		ENST00000395407.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAQR5	ENST00000395407.7	c.-115-3079C>A		intron_variant		1	NM_017705.4	P1
PAQR5	ENST00000558684.5	c.-82+19386C>A		intron_variant		5
PAQR5	ENST00000561153.5	c.-115-3079C>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123407 AN: 151942 Hom.: 52777 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.812 AC: 123445 AN: 152060 Hom.: 52789 Cov.: 31 AF XY: 0.810 AC XY: 60202 AN XY: 74318

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.957

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.849

Alfa AF: 0.876 Hom.: 7488

Bravo AF: 0.788

Asia WGS AF: 0.810 AC: 2816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.43

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: rs12900857; hg19: chr15-69649226;