9-137241747-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_006088.6(TUBB4B):c.84C>T(p.His28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,611,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
TUBB4B
NM_006088.6 synonymous
NM_006088.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.67
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 Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
Variant 9-137241747-C-T is Benign according to our data. Variant chr9-137241747-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2894275.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.67 with no splicing effect.
BS2
High AC in GnomAd4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBB4B | NM_006088.6 | c.84C>T | p.His28= | synonymous_variant | 2/4 | ENST00000340384.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB4B | ENST00000340384.5 | c.84C>T | p.His28= | synonymous_variant | 2/4 | 1 | NM_006088.6 | P1 | |
TUBB4B | ENST00000604929.1 | n.157C>T | non_coding_transcript_exon_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152114Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249112Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135316
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GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459812Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726262
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GnomAD4 genome AF: 0.0000789 AC: 12AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74308
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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 | Invitae | Jan 01, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at