dbSNP rs7245858: PPIAP59:p.Leu93Pro (chr19-50927340-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XM_047439804.1(PPIAP59):c.278T>C(p.Leu93Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0357 in 1,613,640 control chromosomes in the GnomAD database, including 1,336 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 0.049 ( 253 hom., cov: 31)

Exomes 𝑓: 0.034 ( 1083 hom. )

Consequence

PPIAP59
XM_047439804.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.88

Publications

13 publications found

Variant links:

Genes affected

PPIAP59 (HGNC:53683): (peptidylprolyl isomerase A pseudogene 59)

PPIAP59 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=-0.66).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.098 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP59	XM_047439804.1 link	c.278T>C	p.Leu93Pro	missense_variant	Exon 1 of 1		XP_047295760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIAP59	ENST00000596021.1 link	n.232T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.0493

AC:

7493

AN:

152076

Hom.:

252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0270

Gnomad ASJ

AF:

0.0138

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0303

Gnomad FIN

AF:

0.0384

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0327

Gnomad OTH

AF:

0.0378

GnomAD4 exome

AF:

0.0343

AC:

50166

AN:

1461446

Hom.:

1083

Cov.:

AF XY:

0.0342

AC XY:

24895

AN XY:

727026

show subpopulations

African (AFR)

AF:

0.101

AC:

3381

AN:

33470

American (AMR)

AF:

0.0183

AC:

817

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

400

AN:

26132

East Asian (EAS)

AF:

0.0000756

AC:

AN:

39700

South Asian (SAS)

AF:

0.0357

AC:

3083

AN:

86248

European-Finnish (FIN)

AF:

0.0343

AC:

1824

AN:

53150

Middle Eastern (MID)

AF:

0.0302

AC:

174

AN:

5760

European-Non Finnish (NFE)

AF:

0.0343

AC:

38159

AN:

1111896

Other (OTH)

AF:

0.0385

AC:

2325

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

2900

5801

8701

11602

14502

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1478

2956

4434

5912

7390

<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:

0.0493

AC:

7503

AN:

152194

Hom.:

253

Cov.:

AF XY:

0.0495

AC XY:

3686

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.101

AC:

4173

AN:

41490

American (AMR)

AF:

0.0270

AC:

413

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0138

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.0301

AC:

145

AN:

4818

European-Finnish (FIN)

AF:

0.0384

AC:

407

AN:

10608

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0327

AC:

2226

AN:

68018

Other (OTH)

AF:

0.0379

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

358

716

1073

1431

1789

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0377

Hom.:

341

Bravo

AF:

0.0502

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.5

(source)

DANN

Benign

0.63

PhyloP100

4.9

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over