chr4-188146963-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178556.5(TRIML1):c.998C>T(p.Thr333Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000997 in 1,554,264 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178556.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIML1 | NM_178556.5 | c.998C>T | p.Thr333Ile | missense_variant | 6/6 | ENST00000332517.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIML1 | ENST00000332517.4 | c.998C>T | p.Thr333Ile | missense_variant | 6/6 | 1 | NM_178556.5 | P1 | |
TRIML1 | ENST00000507581.5 | n.458C>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
TRIML1 | ENST00000512233.1 | n.348C>T | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152014Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000688 AC: 14AN: 203582Hom.: 0 AF XY: 0.0000652 AC XY: 7AN XY: 107442
GnomAD4 exome AF: 0.000109 AC: 153AN: 1402250Hom.: 0 Cov.: 31 AF XY: 0.0000955 AC XY: 66AN XY: 691020
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152014Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.998C>T (p.T333I) alteration is located in exon 6 (coding exon 6) of the TRIML1 gene. This alteration results from a C to T substitution at nucleotide position 998, causing the threonine (T) at amino acid position 333 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at