chr4-146909073-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031956.4(TTC29):c.353A>T(p.Asp118Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,644 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. D118Y) 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC29 | NM_031956.4 | c.353A>T | p.Asp118Val | missense_variant | 5/13 | ENST00000325106.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC29 | ENST00000325106.9 | c.353A>T | p.Asp118Val | missense_variant | 5/13 | 1 | NM_031956.4 | P4 | |
TTC29 | ENST00000508306.5 | c.353A>T | p.Asp118Val | missense_variant, NMD_transcript_variant | 5/14 | 1 | |||
TTC29 | ENST00000513335.5 | c.431A>T | p.Asp144Val | missense_variant | 6/14 | 2 | |||
TTC29 | ENST00000504425.5 | c.353A>T | p.Asp118Val | missense_variant | 5/13 | 5 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248646Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134850
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461644Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727102
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.353A>T (p.D118V) alteration is located in exon 5 (coding exon 3) of the TTC29 gene. This alteration results from a A to T substitution at nucleotide position 353, causing the aspartic acid (D) at amino acid position 118 to be replaced by a valine (V). 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