chr4-153704257-T-A

Variant names:

• chr4-153704257-T-A
• rs3804100
• NM_001318789.2:c.1350T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003264.5(TLR2):​c.1350T>A​(p.Ser450Arg) 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. Synonymous variant affecting the same amino acid position (i.e. S450S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TLR2 NM_003264.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.21
• Publications: 224 publications found

Genes affected

TLR2 (HGNC:11848): (toll like receptor 2) The protein encoded by this gene is a member of the Toll-like receptor (TLR) family which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. This protein is a cell-surface protein that can form heterodimers with other TLR family members to recognize conserved molecules derived from microorganisms known as pathogen-associated molecular patterns (PAMPs). Activation of TLRs by PAMPs leads to an up-regulation of signaling pathways to modulate the host's inflammatory response. This gene is also thought to promote apoptosis in response to bacterial lipoproteins. This gene has been implicated in the pathogenesis of several autoimmune diseases. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.051962048).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003264.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR2	NM_001318789.2	MANE Select	c.1350T>A	p.Ser450Arg	missense	Exon 3 of 3	NP_001305718.1
	TLR2	NM_001318787.2		c.1350T>A	p.Ser450Arg	missense	Exon 4 of 4	NP_001305716.1
	TLR2	NM_001318790.2		c.1350T>A	p.Ser450Arg	missense	Exon 3 of 3	NP_001305719.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR2	ENST00000642700.2	MANE Select	c.1350T>A	p.Ser450Arg	missense	Exon 3 of 3	ENSP00000494425.1
	TLR2	ENST00000260010.7	TSL:6	c.1350T>A	p.Ser450Arg	missense	Exon 3 of 3	ENSP00000260010.6
	TLR2	ENST00000642580.1		c.1350T>A	p.Ser450Arg	missense	Exon 3 of 3	ENSP00000495339.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.0090
DANN	Benign	0.50
DEOGEN2	Benign	0.19	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.038	N
LIST_S2	Benign	0.79	T
M_CAP	Benign	0.0057	T
MetaRNN	Benign	0.052	T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	0.89	L
PhyloP100		-4.2
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.033
Sift	Benign	0.42	T
Sift4G	Benign	0.48	T
Polyphen		0.0030	B
Vest4		0.065
MutPred		0.43		Gain of MoRF binding (P = 0.0229)
MVP		0.37
MPC		0.074
ClinPred		0.089	T
GERP RS		-11
Varity_R		0.084
gMVP		0.24
Mutation Taster		=91/9	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: rs3804100; hg19: chr4-154625409;