rs9490809
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006073.4(TRDN):c.383C>T(p.Thr128Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000128 in 1,559,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T128S) has been classified as Likely benign.
Frequency
Consequence
NM_006073.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRDN | NM_006073.4 | c.383C>T | p.Thr128Ile | missense_variant | 3/41 | ENST00000334268.9 | |
LOC105377982 | XR_001743833.2 | n.2346-4894G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRDN | ENST00000334268.9 | c.383C>T | p.Thr128Ile | missense_variant | 3/41 | 1 | NM_006073.4 | A2 | |
ENST00000648704.1 | n.449-4960G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151412Hom.: 0 Cov.: 30
GnomAD4 exome AF: 7.10e-7 AC: 1AN: 1407770Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 697608
GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151412Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 73916
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at