rs192423622
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001099274.3(TINF2):c.1166T>C(p.Ile389Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,613,968 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I389K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001099274.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TINF2 | NM_001099274.3 | c.1166T>C | p.Ile389Thr | missense_variant | 8/9 | ENST00000267415.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TINF2 | ENST00000267415.12 | c.1166T>C | p.Ile389Thr | missense_variant | 8/9 | 1 | NM_001099274.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 151962Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 32AN: 249542Hom.: 0 AF XY: 0.0000960 AC XY: 13AN XY: 135382
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 727242
GnomAD4 genome ? AF: 0.000283 AC: 43AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74362
ClinVar
Submissions by phenotype
Dyskeratosis congenita Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 05, 2023 | - - |
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Dec 24, 2021 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 24, 2019 | - - |
TINF2-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 27, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at