7-28956050-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_014817.4(TRIL):​c.1997G>A​(p.Gly666Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,550,120 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G666R) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00018 ( 2 hom. )

Consequence

TRIL
NM_014817.4 missense

Scores

3
2
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.598
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.020411104).
BS2
High Homozygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRILNM_014817.4 linkuse as main transcriptc.1997G>A p.Gly666Glu missense_variant 1/1 ENST00000539664.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRILENST00000539664.3 linkuse as main transcriptc.1997G>A p.Gly666Glu missense_variant 1/1 NM_014817.4 P1

Frequencies

GnomAD3 genomes
AF:
0.000138
AC:
21
AN:
152244
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000349
AC:
51
AN:
146198
Hom.:
0
AF XY:
0.000463
AC XY:
37
AN XY:
79882
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000789
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00157
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000172
Gnomad OTH exome
AF:
0.000691
GnomAD4 exome
AF:
0.000183
AC:
256
AN:
1397758
Hom.:
2
Cov.:
30
AF XY:
0.000224
AC XY:
155
AN XY:
690618
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000109
Gnomad4 ASJ exome
AF:
0.0000396
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00143
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000987
Gnomad4 OTH exome
AF:
0.000394
GnomAD4 genome
AF:
0.000144
AC:
22
AN:
152362
Hom.:
0
Cov.:
34
AF XY:
0.000175
AC XY:
13
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.0000240
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000217
Hom.:
0
Bravo
AF:
0.0000982
ExAC
AF:
0.000213
AC:
24
Asia WGS
AF:
0.00144
AC:
5
AN:
3478

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 submitterclinical testingAmbry GeneticsSep 27, 2021The c.1997G>A (p.G666E) alteration is located in exon 1 (coding exon 1) of the TRIL gene. This alteration results from a G to A substitution at nucleotide position 1997, causing the glycine (G) at amino acid position 666 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.45
BayesDel_addAF
Benign
-0.073
T
BayesDel_noAF
Uncertain
0.090
CADD
Uncertain
24
DANN
Benign
0.96
DEOGEN2
Benign
0.074
T
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.77
T
MetaRNN
Benign
0.020
T
MutationAssessor
Benign
0.81
L
PrimateAI
Pathogenic
0.91
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.16
B
Vest4
0.28
MVP
0.24
GERP RS
3.2
Varity_R
0.17
gMVP
0.67

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: rs562686571; hg19: chr7-28995666; API