rs751339103
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2
The NM_001379200.1(TBX1):c.913C>A(p.Arg305=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,610,426 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. R305R) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX1 | NM_001379200.1 | c.913C>A | p.Arg305= | synonymous_variant | 5/7 | ENST00000649276.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000649276.2 | c.913C>A | p.Arg305= | synonymous_variant | 5/7 | NM_001379200.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000246 AC: 6AN: 243664Hom.: 0 AF XY: 0.0000227 AC XY: 3AN XY: 132264
GnomAD4 exome AF: 0.000134 AC: 195AN: 1458254Hom.: 0 Cov.: 31 AF XY: 0.000132 AC XY: 96AN XY: 725282
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 03, 2017 | - - |
DiGeorge syndrome Benign:1
Likely 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 | Jan 05, 2023 | 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