1-22322994-G-T

Variant names:

• chr1-22322994-G-T
• rs11580218
• ENST00000487348.1:n.338C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000487348.1(PPIAP34):​n.338C>A 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 0.0789 in 1,049,642 control chromosomes in the GnomAD database, including 5,883 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 (2552 hom., cov: 32)
  • Exomes 𝑓: 0.069 (3331 hom.)
• Consequence: PPIAP34 ENST00000487348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575

Genes affected

PPIAP34 (HGNC:53658): (peptidylprolyl isomerase A pseudogene 34)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP34		n.22322994G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIAP34	ENST00000487348.1	n.338C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20830 AN: 151982 Hom.: 2536 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0241

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.117

GnomAD4 exome AF: 0.0690 AC: 61926 AN: 897542 Hom.: 3331 Cov.: 13 AF XY: 0.0665 AC XY: 31208 AN XY: 469478

Gnomad4 AFR exome AF: 0.340

Gnomad4 AMR exome AF: 0.0453

Gnomad4 ASJ exome AF: 0.0464

Gnomad4 EAS exome AF: 0.0000809

Gnomad4 SAS exome AF: 0.0289

Gnomad4 FIN exome AF: 0.0550

Gnomad4 NFE exome AF: 0.0711

Gnomad4 OTH exome AF: 0.0795

GnomAD4 genome AF: 0.137 AC: 20884 AN: 152100 Hom.: 2552 Cov.: 32 AF XY: 0.132 AC XY: 9840 AN XY: 74360

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.0735

Gnomad4 ASJ AF: 0.0450

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0716

Gnomad4 OTH AF: 0.116

Alfa AF: 0.106 Hom.: 1066

Bravo AF: 0.151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	1.6
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11580218; hg19: chr1-22649487;