2-173486230-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP66		n.173486230C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIAP66	ENST00000440938.1	n.133G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

Gnomad4 AFR exome AF: 0.299

Gnomad4 AMR exome AF: 0.0673

Gnomad4 ASJ exome AF: 0.0803

Gnomad4 EAS exome AF: 0.0278

Gnomad4 SAS exome AF: 0.103

Gnomad4 FIN exome AF: 0.0487

Gnomad4 NFE exome AF: 0.0682

Gnomad4 OTH exome AF: 0.0867

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

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.0787

Gnomad4 EAS AF: 0.0339

Gnomad4 SAS AF: 0.0963

Gnomad4 FIN AF: 0.0497

Gnomad4 NFE AF: 0.0733

Gnomad4 OTH AF: 0.117

Alfa AF: 0.132 Hom.: 306

Bravo AF: 0.145

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497392; hg19: chr2-174350958;