chr20-38002675-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001303457.2(TTI1):c.2605C>T(p.Arg869Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,614,206 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R869H) has been classified as Likely benign.
Frequency
Consequence
NM_001303457.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTI1 | NM_001303457.2 | c.2605C>T | p.Arg869Cys | missense_variant | 4/8 | ENST00000373447.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTI1 | ENST00000373447.8 | c.2605C>T | p.Arg869Cys | missense_variant | 4/8 | 1 | NM_001303457.2 | P1 | |
TTI1 | ENST00000373448.6 | c.2605C>T | p.Arg869Cys | missense_variant | 5/9 | 1 | P1 | ||
TTI1 | ENST00000449821.1 | c.2605C>T | p.Arg869Cys | missense_variant | 3/7 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251492Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135922
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727242
GnomAD4 genome AF: 0.000184 AC: 28AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74476
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.2605C>T (p.R869C) alteration is located in exon 5 (coding exon 3) of the TTI1 gene. This alteration results from a C to T substitution at nucleotide position 2605, causing the arginine (R) at amino acid position 869 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at