19-54108093-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013342.4(TFPT):c.575G>T(p.Arg192Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000147 in 1,565,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013342.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFPT | NM_013342.4 | c.575G>T | p.Arg192Met | missense_variant | Exon 5 of 6 | ENST00000391759.6 | NP_037474.1 | |
TFPT | NM_001321792.2 | c.548G>T | p.Arg183Met | missense_variant | Exon 5 of 6 | NP_001308721.1 | ||
TFPT | XM_005278261.2 | c.215G>T | p.Arg72Met | missense_variant | Exon 4 of 5 | XP_005278318.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000127 AC: 18AN: 1413570Hom.: 0 Cov.: 33 AF XY: 0.0000100 AC XY: 7AN XY: 698786
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.575G>T (p.R192M) alteration is located in exon 5 (coding exon 5) of the TFPT gene. This alteration results from a G to T substitution at nucleotide position 575, causing the arginine (R) at amino acid position 192 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