chr9-137241723-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_006088.6(TUBB4B):c.60T>C(p.Phe20=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,457,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006088.6 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBB4B | NM_006088.6 | c.60T>C | p.Phe20= | splice_region_variant, synonymous_variant | 2/4 | ENST00000340384.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB4B | ENST00000340384.5 | c.60T>C | p.Phe20= | splice_region_variant, synonymous_variant | 2/4 | 1 | NM_006088.6 | P1 | |
TUBB4B | ENST00000604929.1 | n.133T>C | splice_region_variant, non_coding_transcript_exon_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247860Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134854
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1457844Hom.: 0 Cov.: 32 AF XY: 0.00000689 AC XY: 5AN XY: 725330
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at