17-15999935-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_017775.4(TTC19):c.87C>T(p.Leu29=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 1,334,500 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L29L) has been classified as Likely benign.
Frequency
Consequence
NM_017775.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC19 | NM_017775.4 | c.87C>T | p.Leu29= | synonymous_variant | 1/10 | ENST00000261647.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC19 | ENST00000261647.10 | c.87C>T | p.Leu29= | synonymous_variant | 1/10 | 1 | NM_017775.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151800Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000434 AC: 1AN: 2304Hom.: 0 AF XY: 0.000725 AC XY: 1AN XY: 1380
GnomAD4 exome AF: 0.0000321 AC: 38AN: 1182700Hom.: 0 Cov.: 30 AF XY: 0.0000333 AC XY: 19AN XY: 570546
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151800Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74154
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 13, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at