rs3006448

Positions:

• chr1-153341677-C-A
• chr1-153341677-C-G
• chr1-153341677-C-T

Variant summary

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

The NM_020393.4(PGLYRP4):​c.575G>T​(p.Gly192Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 1,613,522 control chromosomes in the GnomAD database, including 584,299 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.83 (52725 hom., cov: 34)
  • Exomes 𝑓: 0.85 (531574 hom.)
• Consequence: PGLYRP4 NM_020393.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997

Genes affected

PGLYRP4 (HGNC:30015): (peptidoglycan recognition protein 4) Summary: This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. These proteins are part of the innate immune system and recognize peptidoglycan, a ubiquitous component of bacterial cell walls. This antimicrobial protein binds to murein peptidoglycans of Gram-positive bacteria. [provided by RefSeq, Oct 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=6.112981E-7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGLYRP4	NM_020393.4	c.575G>T	p.Gly192Val	missense_variant	6/9	ENST00000359650.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGLYRP4	ENST00000359650.10	c.575G>T	p.Gly192Val	missense_variant	6/9	1	NM_020393.4	P4
PGLYRP4	ENST00000368739.3	c.563G>T	p.Gly188Val	missense_variant	6/9	5		A1

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126408 AN: 152150 Hom.: 52698 Cov.: 34

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.837

GnomAD3 exomes AF: 0.844 AC: 212238 AN: 251344 Hom.: 89768 AF XY: 0.846 AC XY: 114964 AN XY: 135832

Gnomad AFR exome AF: 0.760

Gnomad AMR exome AF: 0.811

Gnomad ASJ exome AF: 0.838

Gnomad EAS exome AF: 0.868

Gnomad SAS exome AF: 0.844

Gnomad FIN exome AF: 0.891

Gnomad NFE exome AF: 0.854

Gnomad OTH exome AF: 0.848

GnomAD4 exome AF: 0.853 AC: 1245983 AN: 1461254 Hom.: 531574 Cov.: 46 AF XY: 0.853 AC XY: 619791 AN XY: 726938

Gnomad4 AFR exome AF: 0.755

Gnomad4 AMR exome AF: 0.817

Gnomad4 ASJ exome AF: 0.836

Gnomad4 EAS exome AF: 0.889

Gnomad4 SAS exome AF: 0.838

Gnomad4 FIN exome AF: 0.890

Gnomad4 NFE exome AF: 0.856

Gnomad4 OTH exome AF: 0.850

GnomAD4 genome AF: 0.831 AC: 126488 AN: 152268 Hom.: 52725 Cov.: 34 AF XY: 0.834 AC XY: 62072 AN XY: 74448

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.839

Alfa AF: 0.849 Hom.: 137709

Bravo AF: 0.823

TwinsUK AF: 0.855 AC: 3171

ALSPAC AF: 0.860 AC: 3316

ESP6500AA AF: 0.770 AC: 3392

ESP6500EA AF: 0.852 AC: 7323

ExAC AF: 0.845 AC: 102544

EpiCase AF: 0.854

EpiControl AF: 0.848

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.047
BayesDel_addAF	Benign	-0.81	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.084
DEOGEN2	Benign	0.012	T;.
Eigen	Benign	-1.0
Eigen_PC	Benign	-0.81
FATHMM_MKL	Benign	0.015	N
LIST_S2	Benign	0.17	T;T
MetaRNN	Benign	6.1e-7	T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	-2.2	N;.
MutationTaster	Benign	0.84	P;P
PrimateAI	Benign	0.39	T
PROVEAN	Benign	2.7	N;N
REVEL	Benign	0.027
Sift	Benign	0.22	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;B
Vest4		0.11
MPC		0.062
ClinPred		0.0068	T
GERP RS		3.0
Varity_R		0.068
gMVP		0.52

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: rs3006448; hg19: chr1-153314153;