Variant rs10856839 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_030956.4(TLR10):c.-25A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,554,436 control chromosomes in the GnomAD database, including 33,644 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 0.27 ( 6920 hom., cov: 32)

Exomes 𝑓: 0.18 ( 26724 hom. )

Consequence

TLR10
NM_030956.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.103

Variant links:

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]

TLR10 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR10	NM_030956.4 link	c.-25A>C		5_prime_UTR_variant	Exon 4 of 4	ENST00000308973.9	NP_112218.2	Q9BXR5A0A024R9W4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR10	ENST00000308973.9 link	c.-25A>C		5_prime_UTR_variant	Exon 4 of 4	5	NM_030956.4	ENSP00000308925.4		Q9BXR5

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41166

AN:

151922

Hom.:

6887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.202

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.278

GnomAD3 exomes

AF:

0.238

AC:

49930

AN:

209778

Hom.:

6741

AF XY:

0.239

AC XY:

26928

AN XY:

112816

show subpopulations

Gnomad AFR exome

AF:

0.471

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.234

Gnomad EAS exome

AF:

0.205

Gnomad SAS exome

AF:

0.369

Gnomad FIN exome

AF:

0.269

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.233

GnomAD4 exome

AF:

0.179

AC:

250431

AN:

1402394

Hom.:

26724

Cov.:

AF XY:

0.184

AC XY:

127845

AN XY:

692950

show subpopulations

Gnomad4 AFR exome

AF:

0.477

Gnomad4 AMR exome

AF:

0.224

Gnomad4 ASJ exome

AF:

0.227

Gnomad4 EAS exome

AF:

0.183

Gnomad4 SAS exome

AF:

0.363

Gnomad4 FIN exome

AF:

0.259

Gnomad4 NFE exome

AF:

0.148

Gnomad4 OTH exome

AF:

0.212

GnomAD4 genome

AF:

0.271

AC:

41246

AN:

152042

Hom.:

6920

Cov.:

AF XY:

0.274

AC XY:

20390

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.461

Gnomad4 AMR

AF:

0.240

Gnomad4 ASJ

AF:

0.226

Gnomad4 EAS

AF:

0.202

Gnomad4 SAS

AF:

0.363

Gnomad4 FIN

AF:

0.265

Gnomad4 NFE

AF:

0.166

Gnomad4 OTH

AF:

0.281

Alfa

AF:

0.196

Hom.:

4937

Bravo

AF:

0.271

Asia WGS

AF:

0.319

AC:

1112

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.6

DANN

Benign

0.68

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over