6-149513438-T-C

Variant names:

• chr6-149513438-T-C
• rs9373594
• NM_139126.4:c.1080-1136A>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.1080-1136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.055 (260 hom., cov: 18)
• Consequence: PPIL4 NM_139126.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 23 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIL4	NM_139126.4	c.1080-1136A>G		intron_variant	Intron 11 of 12	ENST00000253329.3	NP_624311.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIL4	ENST00000253329.3	c.1080-1136A>G		intron_variant	Intron 11 of 12	1	NM_139126.4	ENSP00000253329.2
PPIL4	ENST00000340881.2	c.-23-1136A>G		intron_variant	Intron 1 of 2	1		ENSP00000344128.2

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 5632 AN: 103290 Hom.: 260 Cov.: 18

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.0111

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0213

Gnomad MID AF: 0.0536

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0545 AC: 5633 AN: 103308 Hom.: 260 Cov.: 18 AF XY: 0.0538 AC XY: 2546 AN XY: 47366

African (AFR) AF: 0.0718 AC: 1959 AN: 27292

American (AMR) AF: 0.0567 AC: 460 AN: 8110

Ashkenazi Jewish (ASJ) AF: 0.0306 AC: 87 AN: 2842

East Asian (EAS) AF: 0.152 AC: 543 AN: 3574

South Asian (SAS) AF: 0.0962 AC: 287 AN: 2982

European-Finnish (FIN) AF: 0.0213 AC: 69 AN: 3244

Middle Eastern (MID) AF: 0.0549 AC: 9 AN: 164

European-Non Finnish (NFE) AF: 0.0401 AC: 2130 AN: 53076

Other (OTH) AF: 0.0622 AC: 81 AN: 1302

Alfa AF: 0.135 Hom.: 719

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.094
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs9373594; hg19: chr6-149834574;