rs79384503

Variant names:

• chr22-21693680-C-G
• rs79384503
• NM_014337.4:c.1140-136C>G

Your query was ambiguous. Multiple possible variants found:

• chr22-21693680-C-G
• chr22-21693680-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014337.4(PPIL2):​c.1140-136C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000538 in 742,910 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000054 (0 hom.)
• Consequence: PPIL2 NM_014337.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957
• Publications: 0 publications found

Genes affected

PPIL2 (HGNC:9261): (peptidylprolyl isomerase like 2) This gene is a member of the cyclophilin family of peptidylprolyl isomerases. The cyclophilins are a highly conserved ubiquitous family, members of which play an important role in protein folding, immunosuppression by cyclosporin A, and infection of HIV-1 virions. This protein interacts with the proteinase inhibitor eglin c and is localized in the nucleus. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014337.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPIL2	NM_014337.4	MANE Select	c.1140-136C>G		intron	N/A	NP_055152.1
	PPIL2	NM_148176.3		c.1140-136C>G		intron	N/A	NP_680481.1
	PPIL2	NM_001317996.2		c.1140-136C>G		intron	N/A	NP_001304925.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPIL2	ENST00000398831.8	TSL:1 MANE Select	c.1140-136C>G		intron	N/A	ENSP00000381812.3
	PPIL2	ENST00000626352.2	TSL:1	c.1140-136C>G		intron	N/A	ENSP00000486725.1
	PPIL2	ENST00000335025.12	TSL:1	c.1140-136C>G		intron	N/A	ENSP00000334553.7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000538 AC: 4 AN: 742910 Hom.: 0 AF XY: 0.00000771 AC XY: 3 AN XY: 388968

African (AFR) AF: 0.00 AC: 0 AN: 19414

American (AMR) AF: 0.00 AC: 0 AN: 39046

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17958

East Asian (EAS) AF: 0.00 AC: 0 AN: 35258

South Asian (SAS) AF: 0.0000468 AC: 3 AN: 64054

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46374

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3432

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 481766

Other (OTH) AF: 0.0000281 AC: 1 AN: 35608

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		-0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs79384503; hg19: chr22-22047969;