22-39421827-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006116.3(TAB1):c.777C>T(p.Ser259Ser) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000028 in 1,461,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006116.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAB1 | NM_006116.3 | c.777C>T | p.Ser259Ser | splice_region_variant, synonymous_variant | Exon 8 of 11 | ENST00000216160.11 | NP_006107.1 | |
TAB1 | NM_153497.3 | c.777C>T | p.Ser259Ser | splice_region_variant, synonymous_variant | Exon 8 of 11 | NP_705717.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAB1 | ENST00000216160.11 | c.777C>T | p.Ser259Ser | splice_region_variant, synonymous_variant | Exon 8 of 11 | 1 | NM_006116.3 | ENSP00000216160.6 | ||
TAB1 | ENST00000331454.3 | c.777C>T | p.Ser259Ser | splice_region_variant, synonymous_variant | Exon 8 of 11 | 1 | ENSP00000333049.3 | |||
TAB1 | ENST00000473491.1 | n.93C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 4 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251228Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135774
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727178
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at