4-146909074-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_031956.4(TTC29):c.352G>T(p.Asp118Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,613,904 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D118V) has been classified as Uncertain significance.
Frequency
Consequence
NM_031956.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC29 | NM_031956.4 | c.352G>T | p.Asp118Tyr | missense_variant | 5/13 | ENST00000325106.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC29 | ENST00000325106.9 | c.352G>T | p.Asp118Tyr | missense_variant | 5/13 | 1 | NM_031956.4 | P4 | |
TTC29 | ENST00000508306.5 | c.352G>T | p.Asp118Tyr | missense_variant, NMD_transcript_variant | 5/14 | 1 | |||
TTC29 | ENST00000513335.5 | c.430G>T | p.Asp144Tyr | missense_variant | 6/14 | 2 | |||
TTC29 | ENST00000504425.5 | c.352G>T | p.Asp118Tyr | missense_variant | 5/13 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000483 AC: 12AN: 248640Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134844
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461640Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727104
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2023 | The c.352G>T (p.D118Y) alteration is located in exon 5 (coding exon 3) of the TTC29 gene. This alteration results from a G to T substitution at nucleotide position 352, causing the aspartic acid (D) at amino acid position 118 to be replaced by a tyrosine (Y). 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