rs111754814
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001379200.1(TBX1):c.519G>A(p.Pro173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000863 in 1,614,192 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts 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. P173P) has been classified as Likely benign.
Frequency
Consequence
NM_001379200.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX1 | NM_001379200.1 | c.519G>A | p.Pro173= | synonymous_variant | 2/7 | ENST00000649276.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000649276.2 | c.519G>A | p.Pro173= | synonymous_variant | 2/7 | NM_001379200.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00207 AC: 315AN: 152244Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000712 AC: 179AN: 251324Hom.: 1 AF XY: 0.000567 AC XY: 77AN XY: 135876
GnomAD4 exome AF: 0.000737 AC: 1078AN: 1461830Hom.: 2 Cov.: 31 AF XY: 0.000667 AC XY: 485AN XY: 727226
GnomAD4 genome ? AF: 0.00207 AC: 315AN: 152362Hom.: 1 Cov.: 33 AF XY: 0.00191 AC XY: 142AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | TBX1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 27, 2017 | - - |
DiGeorge syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2015 | 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