chr6-149523981-T-C

Variant names:

• chr6-149523981-T-C
• rs17087579
• NM_139126.4:c.870+1162A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139126.4(PPIL4):​c.870+1162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,230 control chromosomes in the GnomAD database, including 797 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 0.067 (797 hom., cov: 32)
• Consequence: PPIL4 NM_139126.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 2 publications found

Genes affected

PPIL4 (HGNC:15702): (peptidylprolyl isomerase like 4) This gene is a member of the cyclophilin family of peptidylprolyl isomerases. The cyclophilins are a highly conserved family, members of which play an important role in protein folding, immunosuppression by cyclosporin A, and infection of HIV-1 virions. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIL4	NM_139126.4	c.870+1162A>G		intron_variant	Intron 9 of 12	ENST00000253329.3	NP_624311.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIL4	ENST00000253329.3	c.870+1162A>G		intron_variant	Intron 9 of 12	1	NM_139126.4	ENSP00000253329.2

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10158 AN: 152112 Hom.: 799 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0541

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0488

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0668 AC: 10174 AN: 152230 Hom.: 797 Cov.: 32 AF XY: 0.0673 AC XY: 5010 AN XY: 74444

African (AFR) AF: 0.191 AC: 7941 AN: 41494

American (AMR) AF: 0.0265 AC: 405 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0541 AC: 188 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5186

South Asian (SAS) AF: 0.0907 AC: 437 AN: 4820

European-Finnish (FIN) AF: 0.0223 AC: 237 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 834 AN: 68020

Other (OTH) AF: 0.0482 AC: 102 AN: 2114

Alfa AF: 0.0264 Hom.: 542

Bravo AF: 0.0713

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.051
DANN	Benign	0.64
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs17087579; hg19: chr6-149845117;