chr5-121852139-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_177478.2(FTMT):c.176C>T(p.Thr59Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000812 in 1,600,638 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_177478.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FTMT | NM_177478.2 | c.176C>T | p.Thr59Ile | missense_variant | Exon 1 of 1 | ENST00000321339.3 | NP_803431.1 | |
LOC105379149 | XR_001742862.1 | n.379+10695C>T | intron_variant | Intron 3 of 3 | ||||
LOC105379149 | XR_948712.3 | n.379+10695C>T | intron_variant | Intron 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000175 AC: 4AN: 228658Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 125340
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1448502Hom.: 1 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 720112
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.176C>T (p.T59I) alteration is located in exon 1 (coding exon 1) of the FTMT 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 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