19-18369799-C-G

Variant names:

• chr19-18369799-C-G
• rs7226
• NM_017712.4:c.*6216C>G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001329471.2(PGPEP1):​c.531C>G​(p.Pro177Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: PGPEP1 NM_001329471.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 26 publications found

Genes affected

PGPEP1 (HGNC:13568): (pyroglutamyl-peptidase I) The gene encodes a cysteine protease and member of the peptidase C15 family of proteins. The encoded protein cleaves amino terminal pyroglutamate residues from protein substrates including thyrotropin-releasing hormone and other neuropeptides. Expression of this gene may be downregulated in colorectal cancer, while activity of the encoded protein may be negatively correlated with cancer progression in colorectal cancer patients. Activity of the encoded protease may also be altered in other disease states including in liver cirrhosis, which is associated with reduced protease activity, and in necrozoospermia, which is associated with elevated protease activity. [provided by RefSeq, Jul 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP7: Synonymous conserved (PhyloP=0.262 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329471.2. 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
	PGPEP1	NM_017712.4	MANE Select	c.*6216C>G		3_prime_UTR	Exon 5 of 5	NP_060182.1	Q9NXJ5-1
	PGPEP1	NM_001329471.2		c.531C>G	p.Pro177Pro	synonymous	Exon 5 of 5	NP_001316400.1
	PGPEP1	NM_001308366.2		c.*6290C>G		3_prime_UTR	Exon 5 of 5	NP_001295295.1	S4R2Y9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGPEP1	ENST00000269919.11	TSL:1 MANE Select	c.*6216C>G		3_prime_UTR	Exon 5 of 5	ENSP00000269919.3	Q9NXJ5-1
	PGPEP1	ENST00000597663.2	TSL:3	c.231C>G	p.Pro77Pro	synonymous	Exon 2 of 2	ENSP00000473226.2	M0R3H3
	PGPEP1	ENST00000595552.2	TSL:2	c.*5C>G		3_prime_UTR	Exon 3 of 3	ENSP00000471130.2	M0R0B6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.43
PhyloP100		0.26

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: rs7226; hg19: chr19-18480609;