rs11580218

Positions:

• chr1-22322994-G-A
• chr1-22322994-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.58).
• 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 66 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPIAP34	ENST00000487348.1	n.338C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.00942

Gnomad4 AMR exome AF: 0.0154

Gnomad4 ASJ exome AF: 0.0519

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00694

Gnomad4 FIN exome AF: 0.0106

Gnomad4 NFE exome AF: 0.0374

Gnomad4 OTH exome AF: 0.0300

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

Gnomad4 AFR AF: 0.00987

Gnomad4 AMR AF: 0.0172

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00644

Gnomad4 FIN AF: 0.0100

Gnomad4 NFE AF: 0.0383

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.000538 Hom.: 1066

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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;