9-137241340-C-CCCGCCG
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The ENST00000340384.5(TUBB4B):c.-9_-4dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000726 in 1,590,806 control chromosomes in the GnomAD database, including 6 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00061 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00074 ( 6 hom. )
Consequence
TUBB4B
ENST00000340384.5 5_prime_UTR
ENST00000340384.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.255
Genes affected
TUBB4B (HGNC:20771): (tubulin beta 4B class IVb) Enables double-stranded RNA binding activity. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Located in microtubule. Implicated in Leber congenital amaurosis with early-onset deafness. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
Variant 9-137241340-C-CCCGCCG is Benign according to our data. Variant chr9-137241340-C-CCCGCCG is described in ClinVar as [Likely_benign]. Clinvar id is 3045573.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 93 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBB4B | NM_006088.6 | c.-9_-4dup | 5_prime_UTR_variant | 1/4 | ENST00000340384.5 | NP_006079.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBB4B | ENST00000340384.5 | c.-9_-4dup | 5_prime_UTR_variant | 1/4 | 1 | NM_006088.6 | ENSP00000341289 | P1 | ||
TUBB4B | ENST00000604929.1 | n.65_70dup | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000612 AC: 93AN: 151852Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000773 AC: 160AN: 206972Hom.: 0 AF XY: 0.000762 AC XY: 88AN XY: 115516
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GnomAD4 exome AF: 0.000738 AC: 1062AN: 1438840Hom.: 6 Cov.: 31 AF XY: 0.000771 AC XY: 552AN XY: 715920
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GnomAD4 genome AF: 0.000612 AC: 93AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.000646 AC XY: 48AN XY: 74292
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
TUBB4B-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 08, 2024 | 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). - |
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at