19-15478517-C-T

Variant names:

• chr19-15478517-C-T
• rs959117
• NM_052890.4:c.61+794G>A

Variant summary

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

The NM_052890.4(PGLYRP2):​c.61+794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,934 control chromosomes in the GnomAD database, including 23,763 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 0.56 (23763 hom., cov: 32)
• Consequence: PGLYRP2 NM_052890.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PGLYRP2	NM_052890.4	c.61+794G>A		intron_variant	Intron 1 of 4	ENST00000340880.5	NP_443122.3
PGLYRP2	NM_001363546.1	c.61+794G>A		intron_variant	Intron 1 of 3		NP_001350475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGLYRP2	ENST00000340880.5	c.61+794G>A		intron_variant	Intron 1 of 4	1	NM_052890.4	ENSP00000345968.4
PGLYRP2	ENST00000292609.8	c.61+794G>A		intron_variant	Intron 1 of 3	1		ENSP00000292609.3
PGLYRP2	ENST00000601792.1	c.169+794G>A		intron_variant	Intron 3 of 3	4		ENSP00000472856.2
PGLYRP2	ENST00000594637.1	c.61+794G>A		intron_variant	Intron 2 of 2	4		ENSP00000470112.1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84282 AN: 151816 Hom.: 23753 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.555 AC: 84330 AN: 151934 Hom.: 23763 Cov.: 32 AF XY: 0.560 AC XY: 41601 AN XY: 74260

African (AFR) AF: 0.507 AC: 21024 AN: 41442

American (AMR) AF: 0.643 AC: 9806 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3468

East Asian (EAS) AF: 0.819 AC: 4236 AN: 5172

South Asian (SAS) AF: 0.660 AC: 3178 AN: 4814

European-Finnish (FIN) AF: 0.502 AC: 5290 AN: 10530

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36558 AN: 67938

Other (OTH) AF: 0.586 AC: 1236 AN: 2110

Alfa AF: 0.555 Hom.: 32287

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.24
PhyloP100		-0.24
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

Other links and lift over

dbSNP: rs959117; hg19: chr19-15589328;