rs753613632
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001379200.1(TBX1):c.1424C>T(p.Ala475Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000534 in 1,480,198 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A475T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001379200.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX1 | NM_001379200.1 | c.1424C>T | p.Ala475Val | missense_variant | 7/7 | ENST00000649276.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000649276.2 | c.1424C>T | p.Ala475Val | missense_variant | 7/7 | NM_001379200.1 | A2 | ||
TBX1 | ENST00000332710.8 | c.1397C>T | p.Ala466Val | missense_variant | 9/9 | 1 | P2 | ||
TBX1 | ENST00000329705.11 | c.1009+774C>T | intron_variant | 1 | A2 | ||||
TBX1 | ENST00000359500.7 | c.1009+774C>T | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000726 AC: 11AN: 151494Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000624 AC: 59AN: 94532Hom.: 2 AF XY: 0.000472 AC XY: 26AN XY: 55130
GnomAD4 exome AF: 0.0000512 AC: 68AN: 1328704Hom.: 1 Cov.: 33 AF XY: 0.0000502 AC XY: 33AN XY: 657790
GnomAD4 genome ? AF: 0.0000726 AC: 11AN: 151494Hom.: 0 Cov.: 33 AF XY: 0.0000811 AC XY: 6AN XY: 73968
ClinVar
Submissions by phenotype
DiGeorge syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2023 | - - |
TBX1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 04, 2020 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2022 | 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