5-95464607-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014639.4(SKIC3):c.4695A>C(p.Ter1565TyrextTer6) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000994 in 1,609,840 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. *1565*) has been classified as Likely benign.
Frequency
Consequence
NM_014639.4 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKIC3 | NM_014639.4 | c.4695A>C | p.Ter1565TyrextTer6 | stop_lost | 43/43 | ENST00000358746.7 | |
SKIC3 | XM_047417937.1 | c.4695A>C | p.Ter1565TyrextTer6 | stop_lost | 43/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKIC3 | ENST00000358746.7 | c.4695A>C | p.Ter1565TyrextTer6 | stop_lost | 43/43 | 1 | NM_014639.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 248038Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133968
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1457612Hom.: 1 Cov.: 29 AF XY: 0.0000138 AC XY: 10AN XY: 725060
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 07, 2021 | This sequence change disrupts the translational stop signal of the TTC37 mRNA. It is expected to extend the length of the TTC37 protein by 6 additional amino acid residues. This variant is present in population databases (rs751183327, ExAC 0.01%). This variant has not been reported in the literature in individuals affected with TTC37-related conditions. 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