rs870335

Positions:

• chr15-69312804-G-T

Variant summary

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

The NM_017705.4(PAQR5):​c.-277+13748G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,362 control chromosomes in the GnomAD database, including 13,280 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 0.41 (13280 hom., cov: 30)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

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 (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAQR5	NM_017705.4	c.-277+13748G>T		intron_variant		ENST00000395407.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAQR5	ENST00000395407.7	c.-277+13748G>T		intron_variant		1	NM_017705.4	P1
PAQR5	ENST00000558684.5	c.-243+13748G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62755 AN: 151246 Hom.: 13271 Cov.: 30

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.415 AC: 62805 AN: 151362 Hom.: 13280 Cov.: 30 AF XY: 0.414 AC XY: 30649 AN XY: 73956

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.402

Alfa AF: 0.396 Hom.: 1506

Bravo AF: 0.415

Asia WGS AF: 0.428 AC: 1490 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	0.73
DANN	Benign	0.40

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: rs870335; hg19: chr15-69605143;