11-118658915-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP3BP6_Moderate
The NM_007180.3(TREH):c.1535T>C(p.Met512Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000251 in 1,613,740 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00026 ( 3 hom. )
Consequence
TREH
NM_007180.3 missense
NM_007180.3 missense
Scores
9
5
4
Clinical Significance
Conservation
PhyloP100: 6.05
Genes affected
TREH (HGNC:12266): (trehalase) This gene encodes an enzyme that hydrolyses trehalose, a disaccharide formed from two glucose molecules found mainly in fungi, plants, and insects. A partial duplication of this gene is located adjacent to this locus on chromosome 11. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.832
BP6
?
Variant 11-118658915-A-G is Benign according to our data. Variant chr11-118658915-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3052822.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TREH | NM_007180.3 | c.1535T>C | p.Met512Thr | missense_variant | 13/15 | ENST00000264029.9 | |
TREH | NM_001301065.2 | c.1442T>C | p.Met481Thr | missense_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TREH | ENST00000264029.9 | c.1535T>C | p.Met512Thr | missense_variant | 13/15 | 1 | NM_007180.3 | P1 | |
TREH | ENST00000397925.2 | c.1442T>C | p.Met481Thr | missense_variant | 12/14 | 1 | |||
TREH | ENST00000613915.4 | c.*1312T>C | 3_prime_UTR_variant, NMD_transcript_variant | 11/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152132Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000193 AC: 48AN: 249230Hom.: 0 AF XY: 0.000237 AC XY: 32AN XY: 135212
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GnomAD4 exome AF: 0.000257 AC: 375AN: 1461608Hom.: 3 Cov.: 34 AF XY: 0.000263 AC XY: 191AN XY: 727108
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TREH-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
D
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