chr17-47744192-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_013351.2(TBX21):c.769-3C>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 0.000424 in 1,614,122 control chromosomes in the GnomAD database, including 2 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 Likely benign (★).
Frequency
Consequence
NM_013351.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX21 | NM_013351.2 | c.769-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000177694.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX21 | ENST00000177694.2 | c.769-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_013351.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00231 AC: 352AN: 152210Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000533 AC: 134AN: 251262Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135792
GnomAD4 exome AF: 0.000226 AC: 331AN: 1461794Hom.: 1 Cov.: 32 AF XY: 0.000202 AC XY: 147AN XY: 727210
GnomAD4 genome ? AF: 0.00232 AC: 354AN: 152328Hom.: 1 Cov.: 32 AF XY: 0.00230 AC XY: 171AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at