17-15999807-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The ENST00000475723.5(TTC19):n.4G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000128 in 1,556,896 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 Pathogenic (★).
Frequency
Consequence
ENST00000475723.5 non_coding_transcript_exon
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTC19 | NM_017775.4 | c.-42G>T | upstream_gene_variant | ENST00000261647.10 | NP_060245.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000127 AC: 2AN: 157956Hom.: 0 AF XY: 0.0000115 AC XY: 1AN XY: 87058
GnomAD4 exome AF: 0.0000128 AC: 18AN: 1404680Hom.: 0 Cov.: 30 AF XY: 0.0000187 AC XY: 13AN XY: 695460
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
not provided Pathogenic:1Other:1
c.-42G>T of the TTC19 gene (NM_017775.3) This variant is a nonsense mutation in the TTC19 gene is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Although this mutation has not been reported previously to our knowledge, it is expected to be a pathogenic mutation. The variant is found in LSME-MITOP panel(s). -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at