7-28955763-A-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014817.4(TRIL):c.2284T>A(p.Phe762Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000415 in 1,398,034 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.000041 ( 0 hom. )
Consequence
TRIL
NM_014817.4 missense
NM_014817.4 missense
Scores
2
4
5
Clinical Significance
Conservation
PhyloP100: 3.83
Genes affected
TRIL (HGNC:22200): (TLR4 interactor with leucine rich repeats) TRIL is a component of the TLR4 (MIM 603030) complex and is induced in a number of cell types by lipopolysaccharide (LPS) (Carpenter et al., 2009 [PubMed 19710467]).[supplied by OMIM, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1987328).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIL | NM_014817.4 | c.2284T>A | p.Phe762Ile | missense_variant | 1/1 | ENST00000539664.3 | NP_055632.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIL | ENST00000539664.3 | c.2284T>A | p.Phe762Ile | missense_variant | 1/1 | NM_014817.4 | ENSP00000479256 | P1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD3 exomes AF: 0.00000661 AC: 1AN: 151230Hom.: 0 AF XY: 0.0000124 AC XY: 1AN XY: 80730
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GnomAD4 exome AF: 0.0000415 AC: 58AN: 1398034Hom.: 0 Cov.: 30 AF XY: 0.0000493 AC XY: 34AN XY: 689556
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GnomAD4 genome Cov.: 34
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34
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2021 | The c.2284T>A (p.F762I) alteration is located in exon 1 (coding exon 1) of the TRIL gene. This alteration results from a T to A substitution at nucleotide position 2284, causing the phenylalanine (F) at amino acid position 762 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationAssessor
Benign
L
PrimateAI
Uncertain
T
Sift4G
Uncertain
D
Polyphen
P
Vest4
MVP
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at