Menu
GeneBe

11-118658418-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_007180.3(TREH):c.1623C>T(p.Gly541=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,610,474 control chromosomes in the GnomAD database, including 42,605 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3312 hom., cov: 33)
Exomes 𝑓: 0.23 ( 39293 hom. )

Consequence

TREH
NM_007180.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.05
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-118658418-G-A is Benign according to our data. Variant chr11-118658418-G-A is described in ClinVar as [Benign]. Clinvar id is 3060997.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.05 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TREHNM_007180.3 linkuse as main transcriptc.1623C>T p.Gly541= synonymous_variant 15/15 ENST00000264029.9
TREHNM_001301065.2 linkuse as main transcriptc.1530C>T p.Gly510= synonymous_variant 14/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TREHENST00000264029.9 linkuse as main transcriptc.1623C>T p.Gly541= synonymous_variant 15/151 NM_007180.3 P1O43280-1
TREHENST00000397925.2 linkuse as main transcriptc.1530C>T p.Gly510= synonymous_variant 14/141 O43280-2
TREHENST00000613915.4 linkuse as main transcriptc.*1400C>T 3_prime_UTR_variant, NMD_transcript_variant 13/132

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.203
AC:
30801
AN:
152062
Hom.:
3309
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.174
Gnomad AMR
AF:
0.236
Gnomad ASJ
AF:
0.200
Gnomad EAS
AF:
0.245
Gnomad SAS
AF:
0.356
Gnomad FIN
AF:
0.217
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.228
Gnomad OTH
AF:
0.197
GnomAD3 exomes
AF:
0.230
AC:
56284
AN:
244492
Hom.:
6777
AF XY:
0.238
AC XY:
31665
AN XY:
132866
show subpopulations
Gnomad AFR exome
AF:
0.120
Gnomad AMR exome
AF:
0.209
Gnomad ASJ exome
AF:
0.200
Gnomad EAS exome
AF:
0.247
Gnomad SAS exome
AF:
0.341
Gnomad FIN exome
AF:
0.221
Gnomad NFE exome
AF:
0.224
Gnomad OTH exome
AF:
0.227
GnomAD4 exome
AF:
0.229
AC:
333544
AN:
1458294
Hom.:
39293
Cov.:
34
AF XY:
0.232
AC XY:
168610
AN XY:
725288
show subpopulations
Gnomad4 AFR exome
AF:
0.116
Gnomad4 AMR exome
AF:
0.210
Gnomad4 ASJ exome
AF:
0.202
Gnomad4 EAS exome
AF:
0.221
Gnomad4 SAS exome
AF:
0.337
Gnomad4 FIN exome
AF:
0.221
Gnomad4 NFE exome
AF:
0.226
Gnomad4 OTH exome
AF:
0.230
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.202
AC:
30808
AN:
152180
Hom.:
3312
Cov.:
33
AF XY:
0.206
AC XY:
15320
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.123
Gnomad4 AMR
AF:
0.236
Gnomad4 ASJ
AF:
0.200
Gnomad4 EAS
AF:
0.244
Gnomad4 SAS
AF:
0.358
Gnomad4 FIN
AF:
0.217
Gnomad4 NFE
AF:
0.228
Gnomad4 OTH
AF:
0.198
Alfa
AF:
0.209
Hom.:
1509
Bravo
AF:
0.194
Asia WGS
AF:
0.268
AC:
930
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

TREH-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 21, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
Cadd
Benign
1.5
Dann
Benign
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs7928371; hg19: chr11-118529127; COSMIC: COSV50622216; COSMIC: COSV50622216; API