2-47051835-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020458.4(TTC7A):c.2107C>T(p.Pro703Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,612,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P703P) has been classified as Likely benign.
Frequency
Consequence
NM_020458.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC7A | NM_020458.4 | c.2107C>T | p.Pro703Ser | missense_variant | 18/20 | ENST00000319190.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC7A | ENST00000319190.11 | c.2107C>T | p.Pro703Ser | missense_variant | 18/20 | 2 | NM_020458.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250056Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135368
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1459838Hom.: 0 Cov.: 32 AF XY: 0.0000317 AC XY: 23AN XY: 726280
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
Multiple gastrointestinal atresias Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 16, 2022 | This variant has not been reported in the literature in individuals affected with TTC7A-related conditions. This variant is present in population databases (rs749594871, gnomAD 0.006%). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 703 of the TTC7A protein (p.Pro703Ser). ClinVar contains an entry for this variant (Variation ID: 528458). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at