Variant chr19-50927340-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

Variant links:

Genes affected

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

PPIAP59 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PPIAP59	XM_047439804.1 linkuse as main transcript	c.278T>C	p.Leu93Pro	missense_variant	1/1		XP_047295760.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPIAP59	ENST00000596021.1 linkuse as main transcript	n.232T>C		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0183

Gnomad4 ASJ exome

AF:

0.0153

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0357

Gnomad4 FIN exome

AF:

0.0343

Gnomad4 NFE exome

AF:

0.0343

Gnomad4 OTH exome

AF:

0.0385

GnomAD4 genome

AF:

0.0493

AC:

7503

AN:

152194

Hom.:

253

Cov.:

AF XY:

0.0495

AC XY:

3686

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.0270

Gnomad4 ASJ

AF:

0.0138

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0301

Gnomad4 FIN

AF:

0.0384

Gnomad4 NFE

AF:

0.0327

Gnomad4 OTH

AF:

0.0379

Alfa

AF:

0.0326

Hom.:

175

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

DANN

Benign

0.63

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over