rs3813136

Positions:

• chr19-15480522-A-G
• chr19-15480522-A-T

Variant summary

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

The ENST00000601792.1(PGLYRP2):​c.-9-271T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,972 control chromosomes in the GnomAD database, including 9,305 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 0.35 (9305 hom., cov: 31)
• Consequence: PGLYRP2 ENST00000601792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGLYRP2	ENST00000601792.1	c.-9-271T>C		intron_variant		4		ENSP00000472856

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52761 AN: 151854 Hom.: 9303 Cov.: 31

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.347 AC: 52781 AN: 151972 Hom.: 9305 Cov.: 31 AF XY: 0.347 AC XY: 25766 AN XY: 74292

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.351

Alfa AF: 0.317 Hom.: 3806

Bravo AF: 0.354

Asia WGS AF: 0.427 AC: 1483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813136; hg19: chr19-15591333;