rs12900857

Variant names:

• chr15-69356887-C-A
• rs12900857
• NM_017705.4:c.-115-3079C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-69356887-C-A
• chr15-69356887-C-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.-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
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 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.-115-3079C>A		intron	N/A	NP_060175.3
	PAQR5	NM_001104554.2		c.-115-3079C>A		intron	N/A	NP_001098024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR5	ENST00000395407.7	TSL:1 MANE Select	c.-115-3079C>A		intron	N/A	ENSP00000378803.2
	PAQR5	ENST00000561153.5	TSL:5	c.-115-3079C>A		intron	N/A	ENSP00000453526.1
	PAQR5	ENST00000558684.5	TSL:5	c.-82+19386C>A		intron	N/A	ENSP00000453009.1

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

African (AFR) AF: 0.527 AC: 21809 AN: 41404

American (AMR) AF: 0.812 AC: 12398 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3322 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3757 AN: 5164

South Asian (SAS) AF: 0.940 AC: 4531 AN: 4822

European-Finnish (FIN) AF: 0.888 AC: 9407 AN: 10592

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65316 AN: 68024

Other (OTH) AF: 0.849 AC: 1795 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		-0.19
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: rs12900857; hg19: chr15-69649226;