9-97546240-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003275.4(TMOD1):c.176C>T(p.Thr59Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003275.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMOD1 | NM_003275.4 | c.176C>T | p.Thr59Met | missense_variant | Exon 3 of 10 | ENST00000259365.9 | NP_003266.1 | |
TMOD1 | NM_001166116.2 | c.176C>T | p.Thr59Met | missense_variant | Exon 3 of 10 | NP_001159588.1 | ||
TMOD1 | XM_047423825.1 | c.-131-7041C>T | intron_variant | Intron 1 of 7 | XP_047279781.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152118Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000759 AC: 19AN: 250464Hom.: 1 AF XY: 0.0000590 AC XY: 8AN XY: 135512
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461728Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727154
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152236Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.176C>T (p.T59M) alteration is located in exon 3 (coding exon 2) of the TMOD1 gene. This alteration results from a C to T substitution at nucleotide position 176, causing the threonine (T) at amino acid position 59 to be replaced by a methionine (M). 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