chr11-118667599-G-T

Position:

• chr11-118667599-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000264029.9(TREH):​c.90-4160C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,014 control chromosomes in the GnomAD database, including 8,007 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8007 hom., cov: 32)
• Consequence: TREH ENST00000264029.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TREH	NM_007180.3	c.90-4160C>A		intron_variant		ENST00000264029.9	NP_009111.2
TREH	NM_001301065.2	c.90-4160C>A		intron_variant			NP_001287994.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TREH	ENST00000264029.9	c.90-4160C>A		intron_variant		1	NM_007180.3	ENSP00000264029	P1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47980 AN: 151896 Hom.: 7993 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.331

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.316 AC: 48011 AN: 152014 Hom.: 8007 Cov.: 32 AF XY: 0.316 AC XY: 23489 AN XY: 74290

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.330

Alfa AF: 0.327 Hom.: 1031

Bravo AF: 0.331

Asia WGS AF: 0.268 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs692750; hg19: chr11-118538308;