Variant 4-38775438-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_030956.4(TLR10):c.153G>A(p.Thr51Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 1,613,984 control chromosomes in the GnomAD database, including 4,846 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 ( 1193 hom., cov: 32)

Exomes 𝑓: 0.048 ( 3653 hom. )

Consequence

TLR10
NM_030956.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.30

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP7

Synonymous conserved (PhyloP=-1.3 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR10	NM_030956.4 linkuse as main transcript	c.153G>A	p.Thr51Thr	synonymous_variant	4/4	ENST00000308973.9	NP_112218.2	Q9BXR5A0A024R9W4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR10	ENST00000308973.9 linkuse as main transcript	c.153G>A	p.Thr51Thr	synonymous_variant	4/4	5	NM_030956.4	ENSP00000308925.4		Q9BXR5

Frequencies

GnomAD3 genomes

AF:

0.0953

AC:

14484

AN:

152046

Hom.:

1189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0942

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

GnomAD3 exomes

AF:

0.0842

AC:

21137

AN:

251078

Hom.:

1412

AF XY:

0.0827

AC XY:

11225

AN XY:

135702

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.157

Gnomad ASJ exome

AF:

0.109

Gnomad EAS exome

AF:

0.101

Gnomad SAS exome

AF:

0.156

Gnomad FIN exome

AF:

0.0208

Gnomad NFE exome

AF:

0.0337

Gnomad OTH exome

AF:

0.0807

GnomAD4 exome

AF:

0.0482

AC:

70455

AN:

1461818

Hom.:

3653

Cov.:

AF XY:

0.0511

AC XY:

37174

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.205

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.101

Gnomad4 SAS exome

AF:

0.159

Gnomad4 FIN exome

AF:

0.0232

Gnomad4 NFE exome

AF:

0.0270

Gnomad4 OTH exome

AF:

0.0678

GnomAD4 genome

AF:

0.0953

AC:

14508

AN:

152166

Hom.:

1193

Cov.:

AF XY:

0.0954

AC XY:

7099

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.139

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.0945

Gnomad4 SAS

AF:

0.153

Gnomad4 FIN

AF:

0.0180

Gnomad4 NFE

AF:

0.0301

Gnomad4 OTH

AF:

0.0998

Alfa

AF:

0.0508

Hom.:

486

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

-0.80

CADD

Benign

7.7

DANN

Benign

0.47

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