rs138108276
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001102401.4(TTI2):c.1063C>T(p.Arg355Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00459 in 1,614,010 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R355H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001102401.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTI2 | NM_001102401.4 | c.1063C>T | p.Arg355Cys | missense_variant | 5/8 | ENST00000431156.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTI2 | ENST00000431156.7 | c.1063C>T | p.Arg355Cys | missense_variant | 5/8 | 1 | NM_001102401.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00371 AC: 565AN: 152112Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00308 AC: 773AN: 251170Hom.: 1 AF XY: 0.00296 AC XY: 402AN XY: 135772
GnomAD4 exome AF: 0.00468 AC: 6846AN: 1461780Hom.: 17 Cov.: 32 AF XY: 0.00455 AC XY: 3311AN XY: 727172
GnomAD4 genome ? AF: 0.00371 AC: 565AN: 152230Hom.: 2 Cov.: 32 AF XY: 0.00402 AC XY: 299AN XY: 74426
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | TTI2: BS1 - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 16, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at