Variant chr4-38775552-A-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.39T>A(p.Ile13Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,611,828 control chromosomes in the GnomAD database, including 35,810 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 ( 6921 hom., cov: 32)

Exomes 𝑓: 0.18 ( 28889 hom. )

Consequence

TLR10
NM_030956.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

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=-0.86).

BP7

Synonymous conserved (PhyloP=1.01 with no splicing effect.

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/exons	MANE	Protein	UniProt
TLR10	NM_030956.4 linkuse as main transcript	c.39T>A	p.Ile13Ile	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.39T>A	p.Ile13Ile	synonymous_variant	4/4	5	NM_030956.4	ENSP00000308925.4		Q9BXR5

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41179

AN:

151938

Hom.:

6888

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.201

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.277

GnomAD3 exomes

AF:

0.239

AC:

59402

AN:

248910

Hom.:

8089

AF XY:

0.241

AC XY:

32410

AN XY:

134580

show subpopulations

Gnomad AFR exome

AF:

0.471

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.205

Gnomad SAS exome

AF:

0.369

Gnomad FIN exome

AF:

0.266

Gnomad NFE exome

AF:

0.175

Gnomad OTH exome

AF:

0.232

GnomAD4 exome

AF:

0.182

AC:

266028

AN:

1459772

Hom.:

28889

Cov.:

AF XY:

0.189

AC XY:

137035

AN XY:

726166

show subpopulations

Gnomad4 AFR exome

AF:

0.478

Gnomad4 AMR exome

AF:

0.230

Gnomad4 ASJ exome

AF:

0.229

Gnomad4 EAS exome

AF:

0.184

Gnomad4 SAS exome

AF:

0.367

Gnomad4 FIN exome

AF:

0.260

Gnomad4 NFE exome

AF:

0.150

Gnomad4 OTH exome

AF:

0.216

GnomAD4 genome

AF:

0.271

AC:

41259

AN:

152056

Hom.:

6921

Cov.:

AF XY:

0.274

AC XY:

20403

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.240

Gnomad4 ASJ

AF:

0.226

Gnomad4 EAS

AF:

0.201

Gnomad4 SAS

AF:

0.363

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.166

Gnomad4 OTH

AF:

0.280

Alfa

AF:

0.202

Hom.:

1232

Bravo

AF:

0.271

Asia WGS

AF:

0.318

AC:

1109

AN:

3478

EpiCase

AF:

0.168

EpiControl

AF:

0.169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.2

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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