chr7-28955685-T-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014817.4(TRIL):āc.2362A>Gā(p.Met788Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000258 in 1,549,392 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 (ā ).
Frequency
Genomes: š 0.00013 ( 0 hom., cov: 34)
Exomes š: 0.000014 ( 0 hom. )
Consequence
TRIL
NM_014817.4 missense
NM_014817.4 missense
Scores
4
7
Clinical Significance
Conservation
PhyloP100: -0.173
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.024226189).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIL | NM_014817.4 | c.2362A>G | p.Met788Val | 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.2362A>G | p.Met788Val | missense_variant | 1/1 | NM_014817.4 | ENSP00000479256 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152208Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000199 AC: 3AN: 150806Hom.: 0 AF XY: 0.0000124 AC XY: 1AN XY: 80562
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GnomAD4 exome AF: 0.0000143 AC: 20AN: 1397184Hom.: 0 Cov.: 30 AF XY: 0.0000102 AC XY: 7AN XY: 689170
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GnomAD4 genome AF: 0.000131 AC: 20AN: 152208Hom.: 0 Cov.: 34 AF XY: 0.0000941 AC XY: 7AN XY: 74362
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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 | May 09, 2023 | The c.2362A>G (p.M788V) alteration is located in exon 1 (coding exon 1) of the TRIL gene. This alteration results from a A to G substitution at nucleotide position 2362, causing the methionine (M) at amino acid position 788 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationAssessor
Benign
N
PrimateAI
Uncertain
T
Sift4G
Benign
T
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