chr5-40716416-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012382.3(TTC33):c.518C>T(p.Thr173Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_012382.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC33 | NM_012382.3 | c.518C>T | p.Thr173Met | missense_variant | 5/5 | ENST00000337702.5 | |
TTC33 | XM_011514003.4 | c.518C>T | p.Thr173Met | missense_variant | 5/5 | ||
PTGER4 | XM_017009659.3 | c.*37+19653G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC33 | ENST00000337702.5 | c.518C>T | p.Thr173Met | missense_variant | 5/5 | 1 | NM_012382.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000105 AC: 26AN: 248020Hom.: 0 AF XY: 0.0000744 AC XY: 10AN XY: 134368
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461570Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727062
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.518C>T (p.T173M) alteration is located in exon 5 (coding exon 4) of the TTC33 gene. This alteration results from a C to T substitution at nucleotide position 518, causing the threonine (T) at amino acid position 173 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