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rs78726532

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003265.3(TLR3):c.633+279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0388 in 152,300 control chromosomes in the GnomAD database, including 241 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 0.039 ( 241 hom., cov: 32)

Consequence

TLR3
NM_003265.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19
Variant links:
Genes affected
TLR3 (HGNC:11849): (toll like receptor 3) 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. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. The various TLRs exhibit different patterns of expression. This receptor is most abundantly expressed in placenta and pancreas, and is restricted to the dendritic subpopulation of the leukocytes. It recognizes dsRNA associated with viral infection, and induces the activation of NF-kappaB and the production of type I interferons. It thus plays a role in host defense against multiple viruses. [provided by RefSeq, Jul 2021]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TLR3NM_003265.3 linkuse as main transcriptc.633+279A>G intron_variant ENST00000296795.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TLR3ENST00000296795.8 linkuse as main transcriptc.633+279A>G intron_variant 1 NM_003265.3 P1O15455-1
TLR3ENST00000513189.1 linkuse as main transcriptc.633+279A>G intron_variant 1
TLR3ENST00000698351.1 linkuse as main transcriptc.633+279A>G intron_variant
TLR3ENST00000698352.1 linkuse as main transcriptc.*185+279A>G intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0387
AC:
5894
AN:
152182
Hom.:
239
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.0417
Gnomad AMR
AF:
0.0285
Gnomad ASJ
AF:
0.0334
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00352
Gnomad FIN
AF:
0.00725
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.0136
Gnomad OTH
AF:
0.0339
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0388
AC:
5903
AN:
152300
Hom.:
241
Cov.:
32
AF XY:
0.0371
AC XY:
2766
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.0284
Gnomad4 ASJ
AF:
0.0334
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00373
Gnomad4 FIN
AF:
0.00725
Gnomad4 NFE
AF:
0.0136
Gnomad4 OTH
AF:
0.0331
Alfa
AF:
0.0287
Hom.:
23
Bravo
AF:
0.0442
Asia WGS
AF:
0.0130
AC:
45
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.32
Dann
Benign
0.35

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs78726532; hg19: chr4-187000464; API