chr4-38774483-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2
The NM_030956.4(TLR10):c.1108C>T(p.Gln370Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,598,288 control chromosomes in the GnomAD database, including 25 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0063 ( 13 hom., cov: 32)
Exomes 𝑓: 0.00058 ( 12 hom. )
Consequence
TLR10
NM_030956.4 stop_gained
NM_030956.4 stop_gained
Scores
1
3
3
Clinical Significance
Conservation
PhyloP100: 0.758
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM4
?
Stoplost variant in NM_030956.4 Downstream stopcodon found after 831 codons.
BP6
?
Variant 4-38774483-G-A is Benign according to our data. Variant chr4-38774483-G-A is described in ClinVar as [Benign]. Clinvar id is 775957.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00633 (964/152282) while in subpopulation AFR AF= 0.022 (914/41546). AF 95% confidence interval is 0.0208. There are 13 homozygotes in gnomad4. There are 448 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR10 | NM_030956.4 | c.1108C>T | p.Gln370Ter | stop_gained | 4/4 | ENST00000308973.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR10 | ENST00000308973.9 | c.1108C>T | p.Gln370Ter | stop_gained | 4/4 | 5 | NM_030956.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00632 AC: 961AN: 152164Hom.: 13 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
961
AN:
152164
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00155 AC: 364AN: 234894Hom.: 3 AF XY: 0.00113 AC XY: 143AN XY: 126866
GnomAD3 exomes
AF:
AC:
364
AN:
234894
Hom.:
AF XY:
AC XY:
143
AN XY:
126866
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000576 AC: 833AN: 1446006Hom.: 12 Cov.: 35 AF XY: 0.000495 AC XY: 356AN XY: 718614
GnomAD4 exome
AF:
AC:
833
AN:
1446006
Hom.:
Cov.:
35
AF XY:
AC XY:
356
AN XY:
718614
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00633 AC: 964AN: 152282Hom.: 13 Cov.: 32 AF XY: 0.00602 AC XY: 448AN XY: 74462
GnomAD4 genome
?
AF:
AC:
964
AN:
152282
Hom.:
Cov.:
32
AF XY:
AC XY:
448
AN XY:
74462
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
1
ALSPAC
AF:
AC:
0
ESP6500AA
AF:
AC:
74
ESP6500EA
AF:
AC:
1
ExAC
?
AF:
AC:
222
Asia WGS
AF:
AC:
7
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 submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
D;D;D;D
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at