rs9998678

chr4-38775899-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030956.4(TLR10):c.-187A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0822 in 225,868 control chromosomes in the GnomAD database, including 1,365 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 0.095 (1160 hom., cov: 32)
  • Exomes 𝑓: 0.056 (205 hom.)
• Consequence: TLR10 NM_030956.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

TLR10 (HGNC:15634): (toll like receptor 10) 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 most highly expressed in lymphoid tissues such as spleen, lymph node, thymus, and tonsil. Multiple alternatively spliced transcript variants which encode different protein isoforms have been found for this gene. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR10	NM_030956.4	c.-187A>T		5_prime_UTR_variant	3/4	ENST00000308973.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLR10	ENST00000308973.9	c.-187A>T		5_prime_UTR_variant	3/4	5	NM_030956.4	P1

Frequencies

GnomAD3 genomes AF: 0.0949 AC: 14422 AN: 152036 Hom.: 1156 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0180

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.101

GnomAD4 exome AF: 0.0559 AC: 4118 AN: 73714 Hom.: 205 Cov.: 0 AF XY: 0.0565 AC XY: 2163 AN XY: 38304

Gnomad4 AFR exome AF: 0.190

Gnomad4 AMR exome AF: 0.128

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.100

Gnomad4 SAS exome AF: 0.133

Gnomad4 FIN exome AF: 0.0215

Gnomad4 NFE exome AF: 0.0298

Gnomad4 OTH exome AF: 0.0661

GnomAD4 genome AF: 0.0949 AC: 14446 AN: 152154 Hom.: 1160 Cov.: 32 AF XY: 0.0948 AC XY: 7052 AN XY: 74390

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0944

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0180

Gnomad4 NFE AF: 0.0301

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0677 Hom.: 93

Bravo AF: 0.107

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.51
Dann	Benign	0.40

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

Other links and lift over

dbSNP: rs9998678; hg19: chr4-38777520;