chr4-38774085-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_030956.4(TLR10):c.1506C>T(p.Ser502=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,612,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 0 hom. )
Consequence
TLR10
NM_030956.4 synonymous
NM_030956.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.704
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 4-38774085-G-A is Benign according to our data. Variant chr4-38774085-G-A is described in ClinVar as [Benign]. Clinvar id is 719669.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.704 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR10 | NM_030956.4 | c.1506C>T | p.Ser502= | synonymous_variant | 4/4 | ENST00000308973.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR10 | ENST00000308973.9 | c.1506C>T | p.Ser502= | synonymous_variant | 4/4 | 5 | NM_030956.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00124 AC: 189AN: 152212Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00127 AC: 318AN: 249754Hom.: 0 AF XY: 0.00120 AC XY: 163AN XY: 135336
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GnomAD4 exome AF: 0.00123 AC: 1802AN: 1460174Hom.: 0 Cov.: 35 AF XY: 0.00125 AC XY: 908AN XY: 726020
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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 | Jul 17, 2018 | - - |
Computational scores
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Benign
Cadd
Benign
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at