chr15-69306174-C-T

Position:

• chr15-69306174-C-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+7118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,496 control chromosomes in the GnomAD database, including 16,298 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 0.45 (16298 hom., cov: 30)
• Consequence: PAQR5 NM_017705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAQR5	NM_017705.4	c.-277+7118C>T		intron_variant		ENST00000395407.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAQR5	ENST00000395407.7	c.-277+7118C>T		intron_variant		1	NM_017705.4	P1
PAQR5	ENST00000558684.5	c.-243+7118C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68600 AN: 151378 Hom.: 16265 Cov.: 30

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.374

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.453 AC: 68676 AN: 151496 Hom.: 16298 Cov.: 30 AF XY: 0.455 AC XY: 33692 AN XY: 74030

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.442

Alfa AF: 0.419 Hom.: 1723

Bravo AF: 0.457

Asia WGS AF: 0.528 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.76

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: rs7173355; hg19: chr15-69598513;