8-33509735-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001102401.4(TTI2):c.834+11T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00231 in 1,613,760 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 45 hom., cov: 30)
Exomes 𝑓: 0.0013 ( 39 hom. )
Consequence
TTI2
NM_001102401.4 intron
NM_001102401.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.43
Genes affected
TTI2 (HGNC:26262): (TELO2 interacting protein 2) This gene encodes a regulator of the DNA damage response. The protein is a component of the Triple T complex (TTT) which also includes telomere length regulation protein and TELO2 interacting protein 1. The TTT complex is involved in cellular resistance to DNA damage stresses and may act as a regulator of phosphoinositide-3-kinase-related protein kinase (PIKK) abundance. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 8-33509735-A-C is Benign according to our data. Variant chr8-33509735-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 446028.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0121 (1839/152274) while in subpopulation AFR AF= 0.0421 (1748/41554). AF 95% confidence interval is 0.0404. There are 45 homozygotes in gnomad4. There are 872 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 45 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTI2 | NM_001102401.4 | c.834+11T>G | intron_variant | ENST00000431156.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTI2 | ENST00000431156.7 | c.834+11T>G | intron_variant | 1 | NM_001102401.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0121 AC: 1839AN: 152156Hom.: 45 Cov.: 30
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GnomAD3 exomes AF: 0.00329 AC: 828AN: 251456Hom.: 21 AF XY: 0.00219 AC XY: 298AN XY: 135908
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GnomAD4 exome AF: 0.00129 AC: 1883AN: 1461486Hom.: 39 Cov.: 32 AF XY: 0.00106 AC XY: 772AN XY: 727078
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 03, 2017 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at