chr1-22322994-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000302675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487348.1. 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
	PPIAP34	ENST00000487348.1	TSL:6	n.338C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000302675	ENST00000788801.1		n.453-5889G>T		intron	N/A
	ENSG00000302675	ENST00000788802.1		n.342-6382G>T		intron	N/A

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

African (AFR) AF: 0.340 AC: 7653 AN: 22488

American (AMR) AF: 0.0453 AC: 1981 AN: 43696

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 1046 AN: 22562

East Asian (EAS) AF: 0.0000809 AC: 3 AN: 37066

South Asian (SAS) AF: 0.0289 AC: 2167 AN: 75074

European-Finnish (FIN) AF: 0.0550 AC: 2497 AN: 45422

Middle Eastern (MID) AF: 0.0537 AC: 186 AN: 3466

European-Non Finnish (NFE) AF: 0.0711 AC: 43083 AN: 606122

Other (OTH) AF: 0.0795 AC: 3310 AN: 41646

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

African (AFR) AF: 0.330 AC: 13662 AN: 41438

American (AMR) AF: 0.0735 AC: 1124 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4816

European-Finnish (FIN) AF: 0.0519 AC: 550 AN: 10588

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0716 AC: 4866 AN: 67996

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.119 Hom.: 1991

Bravo AF: 0.151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs11580218; hg19: chr1-22649487;