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GeneBe

rs10790256

chr11-118663373-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_007180.3(TREH):c.156G>A(p.Lys52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,595,466 control chromosomes in the GnomAD database, including 41,336 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 3024 hom., cov: 32)
Exomes 𝑓: 0.23 ( 38312 hom. )

Consequence

TREH
NM_007180.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.65
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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=-0.44).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-118663373-C-T is Benign according to our data. Variant chr11-118663373-C-T is described in ClinVar as [Benign]. Clinvar id is 3035110.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=1.65 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.156G>A p.Lys52= synonymous_variant 2/15 ENST00000264029.9
TREHNM_001301065.2 linkuse as main transcriptc.156G>A p.Lys52= synonymous_variant 2/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TREHENST00000264029.9 linkuse as main transcriptc.156G>A p.Lys52= synonymous_variant 2/151 NM_007180.3 P1O43280-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.183
AC:
27787
AN:
152046
Hom.:
3022
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0561
Gnomad AMI
AF:
0.174
Gnomad AMR
AF:
0.224
Gnomad ASJ
AF:
0.200
Gnomad EAS
AF:
0.244
Gnomad SAS
AF:
0.356
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.227
Gnomad OTH
AF:
0.185
GnomAD3 exomes
AF:
0.221
AC:
49119
AN:
222254
Hom.:
5857
AF XY:
0.230
AC XY:
27473
AN XY:
119590
show subpopulations
Gnomad AFR exome
AF:
0.0495
Gnomad AMR exome
AF:
0.200
Gnomad ASJ exome
AF:
0.197
Gnomad EAS exome
AF:
0.244
Gnomad SAS exome
AF:
0.340
Gnomad FIN exome
AF:
0.218
Gnomad NFE exome
AF:
0.218
Gnomad OTH exome
AF:
0.219
GnomAD4 exome
AF:
0.226
AC:
325950
AN:
1443302
Hom.:
38312
Cov.:
34
AF XY:
0.230
AC XY:
164437
AN XY:
715816
show subpopulations
Gnomad4 AFR exome
AF:
0.0469
Gnomad4 AMR exome
AF:
0.203
Gnomad4 ASJ exome
AF:
0.202
Gnomad4 EAS exome
AF:
0.220
Gnomad4 SAS exome
AF:
0.337
Gnomad4 FIN exome
AF:
0.220
Gnomad4 NFE exome
AF:
0.225
Gnomad4 OTH exome
AF:
0.224
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.183
AC:
27793
AN:
152164
Hom.:
3024
Cov.:
32
AF XY:
0.187
AC XY:
13919
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.0561
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.200
Gnomad4 EAS
AF:
0.243
Gnomad4 SAS
AF:
0.358
Gnomad4 FIN
AF:
0.216
Gnomad4 NFE
AF:
0.227
Gnomad4 OTH
AF:
0.187
Alfa
AF:
0.210
Hom.:
3927
Bravo
AF:
0.172
Asia WGS
AF:
0.266
AC:
924
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
-0.44
Cadd
Benign
11
Dann
Benign
0.66

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: rs10790256; hg19: chr11-118534082; COSMIC: COSV50620151; API