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GeneBe

4-38773784-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_030956.4(TLR10):c.1807C>T(p.Leu603=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00513 in 1,604,216 control chromosomes in the GnomAD database, including 384 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.028 ( 206 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 178 hom. )

Consequence

TLR10
NM_030956.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.18
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 4-38773784-G-A is Benign according to our data. Variant chr4-38773784-G-A is described in ClinVar as [Benign]. Clinvar id is 775956.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.18 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0945 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TLR10NM_030956.4 linkuse as main transcriptc.1807C>T p.Leu603= synonymous_variant 4/4 ENST00000308973.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TLR10ENST00000308973.9 linkuse as main transcriptc.1807C>T p.Leu603= synonymous_variant 4/45 NM_030956.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0279
AC:
4244
AN:
152170
Hom.:
206
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0970
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0105
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000294
Gnomad OTH
AF:
0.0201
GnomAD3 exomes
AF:
0.00734
AC:
1752
AN:
238584
Hom.:
70
AF XY:
0.00534
AC XY:
687
AN XY:
128680
show subpopulations
Gnomad AFR exome
AF:
0.0978
Gnomad AMR exome
AF:
0.00367
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000323
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000248
Gnomad OTH exome
AF:
0.00416
GnomAD4 exome
AF:
0.00274
AC:
3983
AN:
1451928
Hom.:
178
Cov.:
35
AF XY:
0.00227
AC XY:
1641
AN XY:
721826
show subpopulations
Gnomad4 AFR exome
AF:
0.0990
Gnomad4 AMR exome
AF:
0.00453
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000285
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000975
Gnomad4 OTH exome
AF:
0.00604
GnomAD4 genome
AF:
0.0279
AC:
4254
AN:
152288
Hom.:
206
Cov.:
32
AF XY:
0.0274
AC XY:
2043
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.0970
Gnomad4 AMR
AF:
0.0105
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000294
Gnomad4 OTH
AF:
0.0199
Alfa
AF:
0.0122
Hom.:
60
Bravo
AF:
0.0317
Asia WGS
AF:
0.00491
AC:
17
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
2.7
Dann
Benign
0.59

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.

Other links and lift over

dbSNP: rs11466659; hg19: chr4-38775405; API