5-668207-CGACAAGCACACAGAGAGGGGGCCGTGTGGGCGCCGTCAGGGAAGTGCG-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_007030.3(TPPP):c.312-2132_312-2085delCGCACTTCCCTGACGGCGCCCACACGGCCCCCTCTCTGTGTGCTTGTC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 16 hom., cov: 15)
Consequence
TPPP
NM_007030.3 intron
NM_007030.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.275
Genes affected
TPPP (HGNC:24164): (tubulin polymerization promoting protein) Enables several functions, including GTPase activity; magnesium ion binding activity; and protein homodimerization activity. Involved in several processes, including microtubule cytoskeleton organization; negative regulation of tubulin deacetylation; and positive regulation of protein polymerization. Located in several cellular components, including mitochondrion; mitotic spindle; and perinuclear region of cytoplasm. Colocalizes with microtubule and microtubule bundle. [provided by Alliance of Genome Resources, Apr 2022]
CEP72 (HGNC:25547): (centrosomal protein 72) The product of this gene is a member of the leucine-rich-repeat (LRR) superfamily of proteins. The protein is localized to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 5-668207-CGACAAGCACACAGAGAGGGGGCCGTGTGGGCGCCGTCAGGGAAGTGCG-C is Benign according to our data. Variant chr5-668207-CGACAAGCACACAGAGAGGGGGCCGTGTGGGCGCCGTCAGGGAAGTGCG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2655252.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 16 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00237 AC: 221AN: 93216Hom.: 17 Cov.: 15
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00236 AC: 220AN: 93246Hom.: 16 Cov.: 15 AF XY: 0.00229 AC XY: 103AN XY: 45074
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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 | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | TPPP: BS2 - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at