XM_047439804.1:c.278T>C

Variant names:

• chr19-50927340-A-G
• rs7245858
• XM_047439804.1:c.278T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.88
• Publications: 13 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000596021.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPIAP59	ENST00000596021.1	TSL:6	n.232T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7493 AN: 152076 Hom.: 252 Cov.: 31

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.: 34 AF XY: 0.0342 AC XY: 24895 AN XY: 727026

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: 3 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

GnomAD4 genome AF: 0.0493 AC: 7503 AN: 152194 Hom.: 253 Cov.: 31 AF XY: 0.0495 AC XY: 3686 AN XY: 74406

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: 48 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 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: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0327 AC: 2226 AN: 68018

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.0377 Hom.: 341

Bravo AF: 0.0502

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		4.9

Splicing

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

Other links and lift over

dbSNP: rs7245858; hg19: chr19-51430596;