rs3134950

Positions:

• chr6-32159700-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005155.7(PPT2):​c.710+1776C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 150,720 control chromosomes in the GnomAD database, including 31,115 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 0.64 (31115 hom., cov: 28)
• Consequence: PPT2 NM_005155.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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]

PPT2-EGFL8 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPT2	NM_005155.7	c.710+1776C>A		intron_variant		ENST00000324816.11
PPT2-EGFL8	NR_037861.1	n.1124+1776C>A		intron_variant, non_coding_transcript_variant
PPT2	NM_001204103.2	c.710+1776C>A		intron_variant
PPT2	NM_138717.3	c.728+1776C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPT2	ENST00000324816.11	c.710+1776C>A		intron_variant		1	NM_005155.7	P1

Frequencies

GnomAD3 genomes AF: 0.641 AC: 96496 AN: 150622 Hom.: 31099 Cov.: 28

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.641 AC: 96563 AN: 150720 Hom.: 31115 Cov.: 28 AF XY: 0.639 AC XY: 47015 AN XY: 73570

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.686

Alfa AF: 0.639 Hom.: 15794

Bravo AF: 0.648

Asia WGS AF: 0.666 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.083
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs3134950; hg19: chr6-32127477;