rs11955611

Positions:

• chr5-66572090-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

PPIAP78 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PPIAP78		n.66572090C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPIAP78	ENST00000414951.2	n.34C>T		non_coding_transcript_exon_variant	1/1	6

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

Gnomad4 AFR exome AF: 0.258

Gnomad4 AMR exome AF: 0.317

Gnomad4 ASJ exome AF: 0.356

Gnomad4 EAS exome AF: 0.385

Gnomad4 SAS exome AF: 0.340

Gnomad4 FIN exome AF: 0.288

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.274

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.287

Alfa AF: 0.264 Hom.: 2527

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11955611; hg19: chr5-65867918;