6-109420812-G-A

Variant names:

• chr6-109420812-G-A
• rs9487094
• NM_173672.5:c.632-1569C>T

Variant summary

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

The NM_173672.5(PPIL6):​c.632-1569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,092 control chromosomes in the GnomAD database, including 16,953 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 0.45 (16953 hom., cov: 33)
• Consequence: PPIL6 NM_173672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 36 publications found

Genes affected

PPIL6 (HGNC:21557): (peptidylprolyl isomerase like 6) Predicted to enable peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in protein folding and protein peptidyl-prolyl isomerization. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIL6	NM_173672.5	c.632-1569C>T		intron_variant	Intron 5 of 7	ENST00000521072.7	NP_775943.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIL6	ENST00000521072.7	c.632-1569C>T		intron_variant	Intron 5 of 7	1	NM_173672.5	ENSP00000427929.1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 69032 AN: 151974 Hom.: 16925 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.454 AC: 69116 AN: 152092 Hom.: 16953 Cov.: 33 AF XY: 0.454 AC XY: 33710 AN XY: 74330

African (AFR) AF: 0.665 AC: 27584 AN: 41480

American (AMR) AF: 0.420 AC: 6409 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2300 AN: 5184

South Asian (SAS) AF: 0.400 AC: 1932 AN: 4826

European-Finnish (FIN) AF: 0.383 AC: 4045 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24065 AN: 67988

Other (OTH) AF: 0.425 AC: 896 AN: 2110

Alfa AF: 0.385 Hom.: 55349

Bravo AF: 0.467

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.66
PhyloP100		0.33
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: rs9487094; hg19: chr6-109742015;