19-15472833-T-C

Position:

• chr19-15472833-T-C

Variant summary

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

The ENST00000340880.5(PGLYRP2):​c.1133-733A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,100 control chromosomes in the GnomAD database, including 44,757 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 0.76 (44757 hom., cov: 32)
• Consequence: PGLYRP2 ENST00000340880.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

PGLYRP2 (HGNC:30013): (peptidoglycan recognition protein 2) This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. This protein hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in bacterial cell wall glycopeptides, and thus may play a scavenger role by digesting biologically active peptidoglycan into biologically inactive fragments. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGLYRP2	NM_052890.4	c.1133-733A>G		intron_variant		ENST00000340880.5	NP_443122.3
PGLYRP2	NM_001363546.1	c.1133-733A>G		intron_variant			NP_001350475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGLYRP2	ENST00000340880.5	c.1133-733A>G		intron_variant		1	NM_052890.4	ENSP00000345968	P2
PGLYRP2	ENST00000292609.8	c.1133-733A>G		intron_variant		1		ENSP00000292609	A2

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115809 AN: 151982 Hom.: 44702 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.762 AC: 115919 AN: 152100 Hom.: 44757 Cov.: 32 AF XY: 0.758 AC XY: 56377 AN XY: 74346

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.777

Alfa AF: 0.693 Hom.: 3667

Bravo AF: 0.768

Asia WGS AF: 0.668 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.30

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: rs4264508; hg19: chr19-15583644;