ENST00000487348.1:n.338C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000487348.1(PPIAP34):​n.338C>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 0.0293 in 1,049,902 control chromosomes in the GnomAD database, including 614 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 0.024 (66 hom., cov: 32)
  • Exomes 𝑓: 0.030 (548 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=-0.58).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0241 (3660/152126) while in subpopulation NFE AF = 0.0383 (2606/68004). AF 95% confidence interval is 0.0371. There are 66 homozygotes in GnomAd4. There are 1651 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 66 gene

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>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000302675	ENST00000788801.1		n.453-5889G>A		intron	N/A
	ENSG00000302675	ENST00000788802.1		n.342-6382G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0241 AC: 3662 AN: 152008 Hom.: 66 Cov.: 32

Gnomad AFR AF: 0.00987

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00643

Gnomad FIN AF: 0.0100

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0383

Gnomad OTH AF: 0.0225

GnomAD4 exome AF: 0.0302 AC: 27096 AN: 897776 Hom.: 548 Cov.: 13 AF XY: 0.0299 AC XY: 14037 AN XY: 469564

African (AFR) AF: 0.00942 AC: 212 AN: 22496

American (AMR) AF: 0.0154 AC: 673 AN: 43696

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 1170 AN: 22558

East Asian (EAS) AF: 0.00 AC: 0 AN: 37066

South Asian (SAS) AF: 0.00694 AC: 521 AN: 75080

European-Finnish (FIN) AF: 0.0106 AC: 483 AN: 45438

Middle Eastern (MID) AF: 0.0387 AC: 134 AN: 3466

European-Non Finnish (NFE) AF: 0.0374 AC: 22654 AN: 606318

Other (OTH) AF: 0.0300 AC: 1249 AN: 41658

GnomAD4 genome AF: 0.0241 AC: 3660 AN: 152126 Hom.: 66 Cov.: 32 AF XY: 0.0222 AC XY: 1651 AN XY: 74378

African (AFR) AF: 0.00987 AC: 409 AN: 41452

American (AMR) AF: 0.0172 AC: 263 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00644 AC: 31 AN: 4816

European-Finnish (FIN) AF: 0.0100 AC: 106 AN: 10588

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0383 AC: 2606 AN: 68004

Other (OTH) AF: 0.0223 AC: 47 AN: 2110

Alfa AF: 0.000403 Hom.: 1991

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	4.5
DANN	Benign	0.48
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;