Genetic Variant NM_017705.4:c.*88T>C (chr15-69403910-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017705.4(PAQR5):c.*88T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 1,396,354 control chromosomes in the GnomAD database, including 618,142 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 0.84 ( 56167 hom., cov: 32)

Exomes 𝑓: 0.95 ( 561975 hom. )

Consequence

PAQR5
NM_017705.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219

Publications

9 publications found

Variant links:

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]

PAQR5 links:

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

KIF23-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PAQR5	NM_017705.4	MANE Select	c.*88T>C	3_prime_UTR	Exon 9 of 9	NP_060175.3
PAQR5	NM_001104554.2		c.*88T>C	3_prime_UTR	Exon 9 of 9	NP_001098024.1	Q9NXK6
KIF23-AS1	NR_132969.1		n.1249A>G	non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PAQR5	ENST00000395407.7	TSL:1 MANE Select	c.*88T>C	3_prime_UTR	Exon 9 of 9	ENSP00000378803.2	Q9NXK6
PAQR5	ENST00000340965.4	TSL:1	c.*88T>C	3_prime_UTR	Exon 7 of 7	ENSP00000343877.3	Q9NXK6
PAQR5	ENST00000561153.5	TSL:5	c.*88T>C	3_prime_UTR	Exon 9 of 9	ENSP00000453526.1	Q9NXK6

Frequencies

GnomAD3 genomes

AF:

0.845

AC:

128400

AN:

152024

Hom.:

56156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.976

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.964

Gnomad EAS

AF:

0.705

Gnomad SAS

AF:

0.950

Gnomad FIN

AF:

0.923

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.972

Gnomad OTH

AF:

0.875

GnomAD4 exome

AF:

0.947

AC:

1178490

AN:

1244210

Hom.:

561975

Cov.:

AF XY:

0.949

AC XY:

588211

AN XY:

619698

show subpopulations

African (AFR)

AF:

0.617

AC:

17263

AN:

27988

American (AMR)

AF:

0.754

AC:

25582

AN:

33932

Ashkenazi Jewish (ASJ)

AF:

0.971

AC:

20408

AN:

21018

East Asian (EAS)

AF:

0.705

AC:

27038

AN:

38372

South Asian (SAS)

AF:

0.958

AC:

67233

AN:

70162

European-Finnish (FIN)

AF:

0.933

AC:

36008

AN:

38588

Middle Eastern (MID)

AF:

0.943

AC:

4715

AN:

4998

European-Non Finnish (NFE)

AF:

0.974

AC:

931143

AN:

956298

Other (OTH)

AF:

0.929

AC:

49100

AN:

52854

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2724

5448

8173

10897

13621

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18146

36292

54438

72584

90730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.844

AC:

128447

AN:

152144

Hom.:

56167

Cov.:

AF XY:

0.842

AC XY:

62625

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.612

AC:

25357

AN:

41438

American (AMR)

AF:

0.826

AC:

12628

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.964

AC:

3346

AN:

3472

East Asian (EAS)

AF:

0.705

AC:

3647

AN:

5172

South Asian (SAS)

AF:

0.949

AC:

4577

AN:

4824

European-Finnish (FIN)

AF:

0.923

AC:

9792

AN:

10606

Middle Eastern (MID)

AF:

0.922

AC:

271

AN:

294

European-Non Finnish (NFE)

AF:

0.972

AC:

66091

AN:

68026

Other (OTH)

AF:

0.876

AC:

1848

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

829

1658

2487

3316

4145

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

872

1744

2616

3488

4360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.935

Hom.:

273502

Bravo

AF:

0.824

Asia WGS

AF:

0.810

AC:

2817

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.3

(source)

DANN

Benign

0.57

PhyloP100

0.22

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over