rs3813135

Variant names:

• chr19-15476534-T-A
• rs3813135
• NM_052890.4:c.136A>T

Your query was ambiguous. Multiple possible variants found:

• chr19-15476534-T-A
• chr19-15476534-T-C
• chr19-15476534-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_052890.4(PGLYRP2):​c.136A>T​(p.Thr46Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PGLYRP2 NM_052890.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 31 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07347143).

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.136A>T	p.Thr46Ser	missense	Exon 2 of 5	NP_443122.3
	PGLYRP2	NM_001363546.1		c.136A>T	p.Thr46Ser	missense	Exon 2 of 4	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.136A>T	p.Thr46Ser	missense	Exon 2 of 5	ENSP00000345968.4	Q96PD5-1
	PGLYRP2	ENST00000292609.8	TSL:1	c.136A>T	p.Thr46Ser	missense	Exon 2 of 4	ENSP00000292609.3	Q96PD5-2
	PGLYRP2	ENST00000851095.1		c.136A>T	p.Thr46Ser	missense	Exon 2 of 6	ENSP00000521154.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 58

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.085
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.2
DANN	Benign	0.68
DEOGEN2	Benign	0.039	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.040	N
LIST_S2	Benign	0.37	T
M_CAP	Benign	0.0070	T
MetaRNN	Benign	0.073	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.34	N
PhyloP100		-0.033
PrimateAI	Benign	0.28	T
PROVEAN	Benign	0.27	N
REVEL	Benign	0.025
Sift	Uncertain	0.0050	D
Sift4G	Benign	0.36	T
Polyphen		0.0010	B
Vest4		0.085
MutPred		0.15		Gain of disorder (P = 0.0437)
MVP		0.19
MPC		0.15
ClinPred		0.11	T
GERP RS		2.0
Varity_R		0.043
gMVP		0.20
Mutation Taster		=97/3	polymorphism

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: rs3813135; hg19: chr19-15587345;