chr15-69403973-G-T

Variant names:

• chr15-69403973-G-T
• rs3743096
• NM_017705.4:c.*151G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

KIF23-AS1 (HGNC:27075): (KIF23 and PAQR5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

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.*151G>T		3_prime_UTR	Exon 9 of 9	NP_060175.3
	KIF23-AS1	NR_132969.1		n.1186C>A		non_coding_transcript_exon	Exon 2 of 2
	PAQR5	NM_001104554.2		c.*151G>T		3_prime_UTR	Exon 9 of 9	NP_001098024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR5	ENST00000395407.7	TSL:1 MANE Select	c.*151G>T		3_prime_UTR	Exon 9 of 9	ENSP00000378803.2
	PAQR5	ENST00000340965.4	TSL:1	c.*151G>T		3_prime_UTR	Exon 7 of 7	ENSP00000343877.3
	KIF23-AS1	ENST00000558107.2	TSL:3	n.380C>A		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.167 AC: 2738 AN: 16376

American (AMR) AF: 0.133 AC: 2745 AN: 20586

Ashkenazi Jewish (ASJ) AF: 0.00591 AC: 90 AN: 15236

East Asian (EAS) AF: 0.192 AC: 6321 AN: 32858

South Asian (SAS) AF: 0.0212 AC: 1046 AN: 49450

European-Finnish (FIN) AF: 0.0400 AC: 1254 AN: 31342

Middle Eastern (MID) AF: 0.0295 AC: 72 AN: 2442

European-Non Finnish (NFE) AF: 0.0175 AC: 8157 AN: 465202

Other (OTH) AF: 0.0407 AC: 1357 AN: 33374

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

African (AFR) AF: 0.173 AC: 7172 AN: 41486

American (AMR) AF: 0.107 AC: 1639 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.179 AC: 926 AN: 5176

South Asian (SAS) AF: 0.0243 AC: 117 AN: 4820

European-Finnish (FIN) AF: 0.0432 AC: 458 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0188 AC: 1281 AN: 68030

Other (OTH) AF: 0.0636 AC: 134 AN: 2108

Alfa AF: 0.0375 Hom.: 1144

Bravo AF: 0.0873

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		0.38
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: rs3743096; hg19: chr15-69696312;