Variant 11-118658418-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_007180.3(TREH):c.1623C>T(p.Gly541Gly) 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 (no stars).

Frequency

Genomes: 𝑓 0.20 ( 3312 hom., cov: 33)

Exomes 𝑓: 0.23 ( 39293 hom. )

Consequence

TREH
NM_007180.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided 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]

TREH links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

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 no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.05 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 rank	MANE	Protein	UniProt
TREH	NM_007180.3 link	c.1623C>T	p.Gly541Gly	synonymous_variant	Exon 15 of 15	ENST00000264029.9	NP_009111.2	O43280-1
TREH	NM_001301065.2 link	c.1530C>T	p.Gly510Gly	synonymous_variant	Exon 14 of 14		NP_001287994.1	O43280-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TREH	ENST00000264029.9 link	c.1623C>T	p.Gly541Gly	synonymous_variant	Exon 15 of 15	1	NM_007180.3	ENSP00000264029.5	O43280-1
TREH	ENST00000397925.2 link	c.1530C>T	p.Gly510Gly	synonymous_variant	Exon 14 of 14	1		ENSP00000381020.2	O43280-2
TREH	ENST00000613915.4 link	n.*1400C>T		non_coding_transcript_exon_variant	Exon 13 of 13	2		ENSP00000477923.1	A0A087WTJ4
TREH	ENST00000613915.4 link	n.*1400C>T		3_prime_UTR_variant	Exon 13 of 13	2		ENSP00000477923.1	A0A087WTJ4

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30801

AN:

152062

Hom.:

3309

Cov.:

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.:

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

AF:

0.202

AC:

30808

AN:

152180

Hom.:

3312

Cov.:

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: no assertion criteria provided

LINK: link

Submissions by phenotype

TREH-related disorder

Benign:1

Oct 21, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.53

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.

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