22-19764306-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001379200.1(TBX1):c.691C>T(p.Leu231Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,612,690 control chromosomes in the GnomAD database, including 61,245 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX1 | NM_001379200.1 | c.691C>T | p.Leu231Leu | synonymous_variant | Exon 3 of 7 | ENST00000649276.2 | NP_001366129.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX1 | ENST00000649276.2 | c.691C>T | p.Leu231Leu | synonymous_variant | Exon 3 of 7 | NM_001379200.1 | ENSP00000497003.1 |
Frequencies
GnomAD3 genomes AF: 0.337 AC: 51241AN: 152070Hom.: 10388 Cov.: 33
GnomAD3 exomes AF: 0.274 AC: 68669AN: 250178Hom.: 10795 AF XY: 0.274 AC XY: 37096AN XY: 135474
GnomAD4 exome AF: 0.254 AC: 370397AN: 1460502Hom.: 50821 Cov.: 41 AF XY: 0.256 AC XY: 186342AN XY: 726604
GnomAD4 genome AF: 0.337 AC: 51334AN: 152188Hom.: 10424 Cov.: 33 AF XY: 0.335 AC XY: 24945AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:5
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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not provided Benign:3Other:1
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Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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DiGeorge syndrome Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as 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