rs756543718
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001379200.1(TBX1):c.1244G>A(p.Gly415Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000363 in 1,488,368 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G415G) has been classified as Likely benign.
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.1244G>A | p.Gly415Asp | missense_variant | 7/7 | ENST00000649276.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000649276.2 | c.1244G>A | p.Gly415Asp | missense_variant | 7/7 | NM_001379200.1 | A2 | ||
TBX1 | ENST00000332710.8 | c.1217G>A | p.Gly406Asp | missense_variant | 9/9 | 1 | P2 | ||
TBX1 | ENST00000329705.11 | c.1009+594G>A | intron_variant | 1 | A2 | ||||
TBX1 | ENST00000359500.7 | c.1009+594G>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151284Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000327 AC: 38AN: 116340Hom.: 0 AF XY: 0.000239 AC XY: 16AN XY: 66848
GnomAD4 exome AF: 0.0000374 AC: 50AN: 1337084Hom.: 0 Cov.: 33 AF XY: 0.0000332 AC XY: 22AN XY: 662266
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151284Hom.: 0 Cov.: 33 AF XY: 0.0000271 AC XY: 2AN XY: 73838
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2021 | - - |
TBX1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 09, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
DiGeorge syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 06, 2020 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 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