19-54114699-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013342.4(TFPT):c.25A>G(p.Thr9Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013342.4 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFPT | NM_013342.4 | c.25A>G | p.Thr9Ala | missense_variant, splice_region_variant | 2/6 | ENST00000391759.6 | |
TFPT | NM_001321792.2 | c.-3A>G | splice_region_variant, 5_prime_UTR_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFPT | ENST00000391759.6 | c.25A>G | p.Thr9Ala | missense_variant, splice_region_variant | 2/6 | 1 | NM_013342.4 | P1 | |
TFPT | ENST00000391758.5 | c.-3A>G | splice_region_variant, 5_prime_UTR_variant | 2/6 | 1 | ||||
TFPT | ENST00000391757.1 | c.25A>G | p.Thr9Ala | missense_variant, splice_region_variant | 2/6 | 5 | |||
TFPT | ENST00000420715.6 | c.25A>G | p.Thr9Ala | missense_variant, splice_region_variant, NMD_transcript_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.25A>G (p.T9A) alteration is located in exon 2 (coding exon 2) of the TFPT gene. This alteration results from a A to G substitution at nucleotide position 25, causing the threonine (T) at amino acid position 9 to be replaced by an alanine (A). 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
Publications
No publications associated with this variant yet.