Variant rs10790256 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_007180.3(TREH):c.156G>A(p.Lys52Lys) 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 (no stars).

Frequency

Genomes: 𝑓 0.18 ( 3024 hom., cov: 32)

Exomes 𝑓: 0.23 ( 38312 hom. )

Consequence

TREH
NM_007180.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided 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]

TREH links:

TREH (HGNC:):

TREH links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

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 no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.65 with no splicing effect.

BA1

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	Protein	UniProt
TREH	NM_007180.3 linkuse as main transcript	c.156G>A	p.Lys52Lys	synonymous_variant	2/15	ENST00000264029.9	NP_009111.2	O43280-1
TREH	NM_001301065.2 linkuse as main transcript	c.156G>A	p.Lys52Lys	synonymous_variant	2/14		NP_001287994.1	O43280-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TREH	ENST00000264029.9 linkuse as main transcript	c.156G>A	p.Lys52Lys	synonymous_variant	2/15	1	NM_007180.3	ENSP00000264029.5		O43280-1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27787

AN:

152046

Hom.:

3022

Cov.:

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.:

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

AF:

0.183

AC:

27793

AN:

152164

Hom.:

3024

Cov.:

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: no assertion criteria provided

LINK: link

Submissions by phenotype

TREH-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This 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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over