6-32146738-A-T

Variant names:

• chr6-32146738-A-T
• rs9296009
• ENST00000963978.1:c.-9+6A>T

Variant summary

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

The ENST00000963978.1(PPT2):​c.-9+6A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,076 control chromosomes in the GnomAD database, including 3,331 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 0.20 (3331 hom., cov: 31)
• Consequence: PPT2 ENST00000963978.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 47 publications found

Genes affected

PPT2 (HGNC:9326): (palmitoyl-protein thioesterase 2) This gene encodes a member of the palmitoyl-protein thioesterase family. The encoded glycosylated lysosomal protein has palmitoyl-CoA hydrolase activity in vitro, but does not hydrolyze palmitate from cysteine residues in proteins. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream EGFL8 (EGF-like-domain, multiple 8) gene. [provided by RefSeq, Feb 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000963978.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPT2	ENST00000963978.1		c.-9+6A>T		splice_region intron	N/A	ENSP00000634037.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31140 AN: 151958 Hom.: 3329 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.205 AC: 31167 AN: 152076 Hom.: 3331 Cov.: 31 AF XY: 0.207 AC XY: 15373 AN XY: 74330

African (AFR) AF: 0.216 AC: 8969 AN: 41448

American (AMR) AF: 0.217 AC: 3309 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.187 AC: 967 AN: 5176

South Asian (SAS) AF: 0.119 AC: 572 AN: 4824

European-Finnish (FIN) AF: 0.281 AC: 2976 AN: 10576

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13709 AN: 67998

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.198 Hom.: 405

Bravo AF: 0.204

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.8
DANN	Benign	0.87
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs9296009; hg19: chr6-32114515;