chr13-45339541-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003295.4(TPT1):c.355G>T(p.Ala119Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003295.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPT1 | NM_003295.4 | c.355G>T | p.Ala119Ser | missense_variant | 4/6 | ENST00000530705.6 | NP_003286.1 | |
TPT1 | NM_001286272.2 | c.355G>T | p.Ala119Ser | missense_variant | 4/6 | NP_001273201.1 | ||
TPT1 | NM_001286273.2 | c.253G>T | p.Ala85Ser | missense_variant | 3/5 | NP_001273202.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251206Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135770
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461594Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727076
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.355G>T (p.A119S) alteration is located in exon 4 (coding exon 4) of the TPT1 gene. This alteration results from a G to T substitution at nucleotide position 355, causing the alanine (A) at amino acid position 119 to be replaced by a serine (S). 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