19-15472833-T-C

Variant names:

• chr19-15472833-T-C
• rs4264508
• NM_052890.4:c.1133-733A>G

Variant summary

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

The NM_052890.4(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 NM_052890.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052890.4. 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
	PGLYRP2	NM_052890.4	MANE Select	c.1133-733A>G		intron	N/A	NP_443122.3
	PGLYRP2	NM_001363546.1		c.1133-733A>G		intron	N/A	NP_001350475.1	Q96PD5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGLYRP2	ENST00000340880.5	TSL:1 MANE Select	c.1133-733A>G		intron	N/A	ENSP00000345968.4	Q96PD5-1
	PGLYRP2	ENST00000292609.8	TSL:1	c.1133-733A>G		intron	N/A	ENSP00000292609.3	Q96PD5-2
	PGLYRP2	ENST00000851095.1		c.1133-318A>G		intron	N/A	ENSP00000521154.1

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

African (AFR) AF: 0.887 AC: 36843 AN: 41522

American (AMR) AF: 0.708 AC: 10812 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2763 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2905 AN: 5172

South Asian (SAS) AF: 0.703 AC: 3385 AN: 4812

European-Finnish (FIN) AF: 0.688 AC: 7257 AN: 10552

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49381 AN: 67986

Other (OTH) AF: 0.777 AC: 1642 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4264508;

hg19: chr19-15583644;