15-69403973-G-T

Position:

• chr15-69403973-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.*151G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 819,048 control chromosomes in the GnomAD database, including 2,089 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 0.077 (833 hom., cov: 33)
  • Exomes 𝑓: 0.036 (1256 hom.)
• Consequence: PAQR5 NM_017705.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375

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]

KIF23-AS1 (HGNC:):

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 = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAQR5	NM_017705.4	c.*151G>T		3_prime_UTR_variant	9/9	ENST00000395407.7	NP_060175.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAQR5	ENST00000395407.7	c.*151G>T		3_prime_UTR_variant	9/9	1	NM_017705.4	ENSP00000378803.2

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11761 AN: 152064 Hom.: 829 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0638

GnomAD4 exome AF: 0.0357 AC: 23780 AN: 666866 Hom.: 1256 Cov.: 9 AF XY: 0.0338 AC XY: 11621 AN XY: 343390

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.133

Gnomad4 ASJ exome AF: 0.00591

Gnomad4 EAS exome AF: 0.192

Gnomad4 SAS exome AF: 0.0212

Gnomad4 FIN exome AF: 0.0400

Gnomad4 NFE exome AF: 0.0175

Gnomad4 OTH exome AF: 0.0407

GnomAD4 genome AF: 0.0774 AC: 11785 AN: 152182 Hom.: 833 Cov.: 33 AF XY: 0.0792 AC XY: 5896 AN XY: 74400

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0243

Gnomad4 FIN AF: 0.0432

Gnomad4 NFE AF: 0.0188

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0280 Hom.: 272

Bravo AF: 0.0873

Asia WGS AF: 0.0930 AC: 324 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	0.38

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: rs3743096; hg19: chr15-69696312;