rs4830806

Variant names:

• chrX-12913853-C-T
• rs4830806
• NM_138636.5:c.4-5191C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_138636.5(TLR8):​c.4-5191C>T 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 0.52 (11144 hom., 17175 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: TLR8 NM_138636.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958
• Publications: 5 publications found

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]

TLR8-AS1 (HGNC:40720): (TLR8 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR8	NM_138636.5	c.4-5191C>T		intron_variant	Intron 1 of 1	ENST00000218032.7	NP_619542.1
TLR8	NM_016610.4	c.57+3411C>T		intron_variant	Intron 2 of 2		NP_057694.2
TLR8-AS1	NR_030727.1	n.241-5520G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR8	ENST00000218032.7	c.4-5191C>T		intron_variant	Intron 1 of 1	1	NM_138636.5	ENSP00000218032.7
TLR8	ENST00000311912.5	c.57+3411C>T		intron_variant	Intron 2 of 2	1		ENSP00000312082.5

Frequencies

GnomAD3 genomes AF: 0.516 AC: 57262 AN: 110938 Hom.: 11139 Cov.: 24

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.521

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: 0.516 AC: 57306 AN: 110992 Hom.: 11144 Cov.: 24 AF XY: 0.517 AC XY: 17175 AN XY: 33240

African (AFR) AF: 0.672 AC: 20492 AN: 30504

American (AMR) AF: 0.629 AC: 6581 AN: 10466

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1213 AN: 2647

East Asian (EAS) AF: 0.792 AC: 2791 AN: 3523

South Asian (SAS) AF: 0.617 AC: 1638 AN: 2653

European-Finnish (FIN) AF: 0.414 AC: 2441 AN: 5901

Middle Eastern (MID) AF: 0.470 AC: 102 AN: 217

European-Non Finnish (NFE) AF: 0.396 AC: 20932 AN: 52899

Other (OTH) AF: 0.524 AC: 789 AN: 1505

Alfa AF: 0.461 Hom.: 3280

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.23
PhyloP100		-0.96
Mutation Taster		=100/0	polymorphism (auto)

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: rs4830806; hg19: chrX-12931972;