1-39883350-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017646.6(TRIT1):c.142G>A(p.Gly48Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000686 in 1,458,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017646.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIT1 | ENST00000316891.10 | c.142G>A | p.Gly48Ser | missense_variant | Exon 1 of 11 | 1 | NM_017646.6 | ENSP00000321810.5 | ||
TRIT1 | ENST00000372818.5 | c.142G>A | p.Gly48Ser | missense_variant | Exon 1 of 10 | 1 | ENSP00000361905.1 | |||
TRIT1 | ENST00000462797.5 | n.142G>A | non_coding_transcript_exon_variant | Exon 1 of 10 | 5 | ENSP00000473773.1 | ||||
TRIT1 | ENST00000486825.6 | n.124G>A | non_coding_transcript_exon_variant | Exon 1 of 8 | 5 | ENSP00000474151.1 | ||||
TRIT1 | ENST00000489945.5 | n.142G>A | non_coding_transcript_exon_variant | Exon 1 of 7 | 5 | ENSP00000473745.1 | ||||
TRIT1 | ENST00000492612.6 | n.130G>A | non_coding_transcript_exon_variant | Exon 1 of 9 | 5 | ENSP00000473708.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241354Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131556
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1458724Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 725560
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.142G>A (p.G48S) alteration is located in exon 1 (coding exon 1) of the TRIT1 gene. This alteration results from a G to A substitution at nucleotide position 142, causing the glycine (G) at amino acid position 48 to be replaced by a serine (S). 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