chr11-1277074-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_019009.4(TOLLIP):c.790A>G(p.Ile264Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00315 in 1,614,038 control chromosomes in the GnomAD database, including 159 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.016 ( 81 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 78 hom. )
Consequence
TOLLIP
NM_019009.4 missense
NM_019009.4 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 2.87
Genes affected
TOLLIP (HGNC:16476): (toll interacting protein) This gene encodes a ubiquitin-binding protein that interacts with several Toll-like receptor (TLR) signaling cascade components. The encoded protein regulates inflammatory signaling and is involved in interleukin-1 receptor trafficking and in the turnover of IL1R-associated kinase. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004539937).
BP6
?
Variant 11-1277074-T-C is Benign according to our data. Variant chr11-1277074-T-C is described in ClinVar as [Benign]. Clinvar id is 719474.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOLLIP | NM_019009.4 | c.790A>G | p.Ile264Val | missense_variant | 6/6 | ENST00000317204.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOLLIP | ENST00000317204.11 | c.790A>G | p.Ile264Val | missense_variant | 6/6 | 1 | NM_019009.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0163 AC: 2482AN: 152210Hom.: 81 Cov.: 33
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GnomAD3 exomes AF: 0.00411 AC: 1032AN: 251208Hom.: 32 AF XY: 0.00293 AC XY: 398AN XY: 135824
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GnomAD4 exome AF: 0.00177 AC: 2592AN: 1461710Hom.: 78 Cov.: 31 AF XY: 0.00152 AC XY: 1103AN XY: 727156
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GnomAD4 genome ? AF: 0.0163 AC: 2489AN: 152328Hom.: 81 Cov.: 33 AF XY: 0.0151 AC XY: 1126AN XY: 74490
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ESP6500AA
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ExAC
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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 | May 31, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
D;T;D;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;.;B;.
Vest4
MVP
MPC
ClinPred
T
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