ENST00000601792.1:c.-9-271T>C

Variant names:

• chr19-15480522-A-G
• rs3813136
• ENST00000601792.1:c.-9-271T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGLYRP2	ENST00000601792.1	c.-9-271T>C		intron_variant	Intron 1 of 3	4		ENSP00000472856.2

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

African (AFR) AF: 0.330 AC: 13683 AN: 41480

American (AMR) AF: 0.392 AC: 5978 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3466

East Asian (EAS) AF: 0.521 AC: 2668 AN: 5122

South Asian (SAS) AF: 0.429 AC: 2065 AN: 4812

European-Finnish (FIN) AF: 0.292 AC: 3089 AN: 10578

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22582 AN: 67928

Other (OTH) AF: 0.351 AC: 742 AN: 2114

Alfa AF: 0.320 Hom.: 4256

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
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs3813136; hg19: chr19-15591333;