11-118658925-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_007180.3(TREH):c.1525A>T(p.Lys509*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,613,800 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_007180.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TREH | ENST00000264029.9 | c.1525A>T | p.Lys509* | stop_gained | Exon 13 of 15 | 1 | NM_007180.3 | ENSP00000264029.5 | ||
TREH | ENST00000397925.2 | c.1432A>T | p.Lys478* | stop_gained | Exon 12 of 14 | 1 | ENSP00000381020.2 | |||
TREH | ENST00000613915.4 | n.*1302A>T | non_coding_transcript_exon_variant | Exon 11 of 13 | 2 | ENSP00000477923.1 | ||||
TREH | ENST00000613915.4 | n.*1302A>T | 3_prime_UTR_variant | Exon 11 of 13 | 2 | ENSP00000477923.1 |
Frequencies
GnomAD3 genomes AF: 0.000743 AC: 113AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000449 AC: 112AN: 249248Hom.: 0 AF XY: 0.000458 AC XY: 62AN XY: 135230
GnomAD4 exome AF: 0.00125 AC: 1826AN: 1461638Hom.: 3 Cov.: 34 AF XY: 0.00125 AC XY: 906AN XY: 727120
GnomAD4 genome AF: 0.000743 AC: 113AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.000538 AC XY: 40AN XY: 74338
ClinVar
Submissions by phenotype
TREH-related disorder Uncertain:1
The TREH c.1525A>T variant is predicted to result in premature protein termination (p.Lys509*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.097% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at