6-166160974-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001366285.2(TBXT):c.908-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00562 in 1,613,648 control chromosomes in the GnomAD database, including 429 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_001366285.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBXT | NM_001366285.2 | c.908-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000366876.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXT | ENST00000366876.7 | c.908-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001366285.2 | P4 | |||
TBXT | ENST00000366871.7 | c.731-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
TBXT | ENST00000296946.6 | c.905-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0303 AC: 4615AN: 152142Hom.: 230 Cov.: 33
GnomAD3 exomes AF: 0.00768 AC: 1930AN: 251202Hom.: 90 AF XY: 0.00557 AC XY: 756AN XY: 135738
GnomAD4 exome AF: 0.00305 AC: 4451AN: 1461388Hom.: 199 Cov.: 33 AF XY: 0.00260 AC XY: 1888AN XY: 726970
GnomAD4 genome AF: 0.0303 AC: 4616AN: 152260Hom.: 230 Cov.: 33 AF XY: 0.0290 AC XY: 2162AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at