rs2109134

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000218032.7(TLR8):​c.3+2358T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.91 ( 32285 hom., 29644 hem., cov: 22)
Failed GnomAD Quality Control

Consequence

TLR8
ENST00000218032.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0350
Variant links:
Genes affected
TLR8 (HGNC:15632): (toll like receptor 8) 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 gene is predominantly expressed in lung and peripheral blood leukocytes, and lies in close proximity to another family member, TLR7, on chromosome X. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TLR8NM_138636.5 linkuse as main transcriptc.3+2358T>A intron_variant ENST00000218032.7 NP_619542.1
TLR8-AS1NR_030727.1 linkuse as main transcriptn.241-734A>T intron_variant, non_coding_transcript_variant
TLR8NM_016610.4 linkuse as main transcriptc.-80-1239T>A intron_variant NP_057694.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TLR8ENST00000218032.7 linkuse as main transcriptc.3+2358T>A intron_variant 1 NM_138636.5 ENSP00000218032 P2Q9NR97-1
TLR8ENST00000311912.5 linkuse as main transcriptc.-80-1239T>A intron_variant 1 ENSP00000312082 A2Q9NR97-2

Frequencies

GnomAD3 genomes
AF:
0.911
AC:
100432
AN:
110188
Hom.:
32288
Cov.:
22
AF XY:
0.914
AC XY:
29585
AN XY:
32354
show subpopulations
Gnomad AFR
AF:
0.878
Gnomad AMI
AF:
0.897
Gnomad AMR
AF:
0.938
Gnomad ASJ
AF:
0.916
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.945
Gnomad FIN
AF:
0.938
Gnomad MID
AF:
0.862
Gnomad NFE
AF:
0.915
Gnomad OTH
AF:
0.910
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.911
AC:
100483
AN:
110245
Hom.:
32285
Cov.:
22
AF XY:
0.914
AC XY:
29644
AN XY:
32421
show subpopulations
Gnomad4 AFR
AF:
0.879
Gnomad4 AMR
AF:
0.938
Gnomad4 ASJ
AF:
0.916
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.943
Gnomad4 FIN
AF:
0.938
Gnomad4 NFE
AF:
0.915
Gnomad4 OTH
AF:
0.911
Alfa
AF:
0.915
Hom.:
8180
Bravo
AF:
0.911

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.3
DANN
Benign
0.76

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: rs2109134; hg19: chrX-12927186; API