ENST00000440938.1:n.133G>A

Variant names:

• chr2-173486230-C-T
• rs10497392
• ENST00000440938.1:n.133G>A

Variant summary

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

The ENST00000440938.1(PPIAP66):​n.133G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0874 in 796,496 control chromosomes in the GnomAD database, including 4,800 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 0.14 (2204 hom., cov: 32)
  • Exomes 𝑓: 0.076 (2596 hom.)
• Consequence: PPIAP66 ENST00000440938.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.59
• Publications: 2 publications found

Genes affected

PPIAP66 (HGNC:53690): (peptidylprolyl isomerase A pseudogene 66)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440938.1. 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
	PPIAP66	ENST00000440938.1	TSL:6	n.133G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20551 AN: 152026 Hom.: 2201 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.118

GnomAD4 exome AF: 0.0761 AC: 49022 AN: 644352 Hom.: 2596 Cov.: 6 AF XY: 0.0769 AC XY: 26916 AN XY: 349954

African (AFR) AF: 0.299 AC: 5266 AN: 17624

American (AMR) AF: 0.0673 AC: 2896 AN: 43042

Ashkenazi Jewish (ASJ) AF: 0.0803 AC: 1635 AN: 20352

East Asian (EAS) AF: 0.0278 AC: 972 AN: 34902

South Asian (SAS) AF: 0.103 AC: 7241 AN: 70236

European-Finnish (FIN) AF: 0.0487 AC: 2453 AN: 50340

Middle Eastern (MID) AF: 0.105 AC: 428 AN: 4094

European-Non Finnish (NFE) AF: 0.0682 AC: 25300 AN: 371092

Other (OTH) AF: 0.0867 AC: 2831 AN: 32670

GnomAD4 genome AF: 0.135 AC: 20564 AN: 152144 Hom.: 2204 Cov.: 32 AF XY: 0.133 AC XY: 9869 AN XY: 74382

African (AFR) AF: 0.302 AC: 12516 AN: 41440

American (AMR) AF: 0.0868 AC: 1326 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3468

East Asian (EAS) AF: 0.0339 AC: 176 AN: 5194

South Asian (SAS) AF: 0.0963 AC: 465 AN: 4828

European-Finnish (FIN) AF: 0.0497 AC: 527 AN: 10608

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0733 AC: 4986 AN: 68018

Other (OTH) AF: 0.117 AC: 247 AN: 2108

Alfa AF: 0.138 Hom.: 348

Bravo AF: 0.145

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	1.7
DANN	Benign	0.30
PhyloP100		5.6

Splicing

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

Other links and lift over

dbSNP: rs10497392; hg19: chr2-174350958;