chr14-24240759-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001099274.3(TINF2):c.721C>T(p.Pro241Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,613,606 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P241P) has been classified as Likely benign.
Frequency
Consequence
NM_001099274.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TINF2 | NM_001099274.3 | c.721C>T | p.Pro241Ser | missense_variant | 6/9 | ENST00000267415.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TINF2 | ENST00000267415.12 | c.721C>T | p.Pro241Ser | missense_variant | 6/9 | 1 | NM_001099274.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00632 AC: 962AN: 152176Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00165 AC: 409AN: 247808Hom.: 5 AF XY: 0.00112 AC XY: 151AN XY: 134574
GnomAD4 exome AF: 0.000675 AC: 987AN: 1461312Hom.: 12 Cov.: 32 AF XY: 0.000552 AC XY: 401AN XY: 726938
GnomAD4 genome ? AF: 0.00640 AC: 974AN: 152294Hom.: 9 Cov.: 32 AF XY: 0.00598 AC XY: 445AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 11, 2020 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 06, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21199492, 30964210) - |
Dyskeratosis congenita Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
TINF2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 02, 2019 | This variant is classified as 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