rs11955611

Variant names:

• chr5-66572090-C-T
• rs11955611
• ENST00000414951.2:n.34C>T

Variant summary

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

The ENST00000414951.2(PPIAP78):​n.34C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,111,190 control chromosomes in the GnomAD database, including 40,164 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 0.27 (5853 hom., cov: 33)
  • Exomes 𝑓: 0.26 (34311 hom.)
• Consequence: PPIAP78 ENST00000414951.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 0 publications found

Genes affected

PPIAP78 (HGNC:53702): (peptidylprolyl isomerase A pseudogene 78)

ENSG00000304982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP78		n.66572090C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIAP78	ENST00000414951.2	n.34C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000304982	ENST00000807539.1	n.64-19459C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41515 AN: 152030 Hom.: 5850 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.264 AC: 252966 AN: 959042 Hom.: 34311 Cov.: 13 AF XY: 0.267 AC XY: 130962 AN XY: 490346

African (AFR) AF: 0.258 AC: 5692 AN: 22036

American (AMR) AF: 0.317 AC: 12390 AN: 39102

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 6328 AN: 17790

East Asian (EAS) AF: 0.385 AC: 7778 AN: 20214

South Asian (SAS) AF: 0.340 AC: 26514 AN: 78064

European-Finnish (FIN) AF: 0.288 AC: 10604 AN: 36762

Middle Eastern (MID) AF: 0.332 AC: 1411 AN: 4254

European-Non Finnish (NFE) AF: 0.244 AC: 171739 AN: 702532

Other (OTH) AF: 0.274 AC: 10510 AN: 38288

GnomAD4 genome AF: 0.273 AC: 41548 AN: 152148 Hom.: 5853 Cov.: 33 AF XY: 0.279 AC XY: 20711 AN XY: 74366

African (AFR) AF: 0.261 AC: 10853 AN: 41508

American (AMR) AF: 0.307 AC: 4690 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3472

East Asian (EAS) AF: 0.388 AC: 2000 AN: 5160

South Asian (SAS) AF: 0.358 AC: 1728 AN: 4828

European-Finnish (FIN) AF: 0.289 AC: 3053 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17020 AN: 67998

Other (OTH) AF: 0.287 AC: 606 AN: 2112

Alfa AF: 0.263 Hom.: 2903

Bravo AF: 0.272

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	3.5
DANN	Benign	0.81
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs11955611; hg19: chr5-65867918;