chr15-42745313-G-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_173500.4(TTBK2):c.*482C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 186,116 control chromosomes in the GnomAD database, including 659 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.061 ( 640 hom., cov: 32)
Exomes 𝑓: 0.019 ( 19 hom. )
Consequence
TTBK2
NM_173500.4 3_prime_UTR
NM_173500.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.127
Genes affected
TTBK2 (HGNC:19141): (tau tubulin kinase 2) This gene encodes a serine-threonine kinase that putatively phosphorylates tau and tubulin proteins. Mutations in this gene cause spinocerebellar ataxia type 11 (SCA11); a neurodegenerative disease characterized by progressive ataxia and atrophy of the cerebellum and brainstem. [provided by RefSeq, Aug 2009]
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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 15-42745313-G-C is Benign according to our data. Variant chr15-42745313-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 315973.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTBK2 | NM_173500.4 | c.*482C>G | 3_prime_UTR_variant | 15/15 | ENST00000267890.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTBK2 | ENST00000267890.11 | c.*482C>G | 3_prime_UTR_variant | 15/15 | 5 | NM_173500.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0605 AC: 9201AN: 152120Hom.: 638 Cov.: 32
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GnomAD4 exome AF: 0.0193 AC: 654AN: 33880Hom.: 19 Cov.: 0 AF XY: 0.0198 AC XY: 353AN XY: 17840
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GnomAD4 genome AF: 0.0606 AC: 9222AN: 152236Hom.: 640 Cov.: 32 AF XY: 0.0587 AC XY: 4371AN XY: 74432
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spinocerebellar ataxia type 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
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BayesDel_noAF
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