chr9-137241379-T-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_006088.6(TUBB4B):c.19T>G(p.Leu7Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TUBB4B
NM_006088.6 missense
NM_006088.6 missense
Scores
2
1
15
Clinical Significance
Conservation
PhyloP100: -0.441
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 -1 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, TUBB4B
BP4
?
Computational evidence support a benign effect (MetaRNN=0.21295905).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBB4B | NM_006088.6 | c.19T>G | p.Leu7Val | missense_variant | 1/4 | ENST00000340384.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB4B | ENST00000340384.5 | c.19T>G | p.Leu7Val | missense_variant | 1/4 | 1 | NM_006088.6 | P1 | |
TUBB4B | ENST00000604929.1 | n.92T>G | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 3AN: 150798Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 genomes
?
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3
AN:
150798
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Cov.:
33
FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00104 AC: 1448AN: 1389904Hom.: 0 Cov.: 32 AF XY: 0.000995 AC XY: 689AN XY: 692618
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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1448
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1389904
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32
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689
AN XY:
692618
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000199 AC: 3AN: 150918Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73748
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of disorder (P = 0.2136);
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at