rs745663
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_007180.3(TREH):c.1545+19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 1,612,934 control chromosomes in the GnomAD database, including 88,396 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.32 ( 7903 hom., cov: 33)
Exomes 𝑓: 0.33 ( 80493 hom. )
Consequence
TREH
NM_007180.3 intron
NM_007180.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.857
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
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 11-118658886-A-G is Benign according to our data. Variant chr11-118658886-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TREH | NM_007180.3 | c.1545+19T>C | intron_variant | ENST00000264029.9 | NP_009111.2 | |||
TREH | NM_001301065.2 | c.1452+19T>C | intron_variant | NP_001287994.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TREH | ENST00000264029.9 | c.1545+19T>C | intron_variant | 1 | NM_007180.3 | ENSP00000264029.5 | ||||
TREH | ENST00000397925.2 | c.1452+19T>C | intron_variant | 1 | ENSP00000381020.2 | |||||
TREH | ENST00000613915.4 | n.*1322+19T>C | intron_variant | 2 | ENSP00000477923.1 |
Frequencies
GnomAD3 genomes AF: 0.315 AC: 47920AN: 151996Hom.: 7891 Cov.: 33
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GnomAD3 exomes AF: 0.347 AC: 86381AN: 248982Hom.: 16545 AF XY: 0.331 AC XY: 44755AN XY: 135068
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GnomAD4 exome AF: 0.326 AC: 475566AN: 1460820Hom.: 80493 Cov.: 34 AF XY: 0.320 AC XY: 232864AN XY: 726730
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GnomAD4 genome AF: 0.315 AC: 47951AN: 152114Hom.: 7903 Cov.: 33 AF XY: 0.315 AC XY: 23454AN XY: 74356
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at