chr22-19766452-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001379200.1(TBX1):c.1100C>T(p.Pro367Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000045 in 1,333,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001379200.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX1 | NM_001379200.1 | c.1100C>T | p.Pro367Leu | missense_variant | Exon 7 of 7 | ENST00000649276.2 | NP_001366129.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000649276.2 | c.1100C>T | p.Pro367Leu | missense_variant | Exon 7 of 7 | NM_001379200.1 | ENSP00000497003.1 | |||
TBX1 | ENST00000332710.8 | c.1073C>T | p.Pro358Leu | missense_variant | Exon 9 of 9 | 1 | ENSP00000331791.4 | |||
TBX1 | ENST00000329705.11 | c.1009+450C>T | intron_variant | Intron 8 of 8 | 1 | ENSP00000331176.7 | ||||
TBX1 | ENST00000359500.7 | c.1009+450C>T | intron_variant | Intron 8 of 9 | 1 | ENSP00000352483.3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151250Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000338 AC: 4AN: 1182036Hom.: 0 Cov.: 21 AF XY: 0.00000345 AC XY: 2AN XY: 579114
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151250Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73858
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at