17-47733780-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_013351.2(TBX21):c.326C>G(p.Ala109Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,543,306 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013351.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX21 | NM_013351.2 | c.326C>G | p.Ala109Gly | missense_variant | 1/6 | ENST00000177694.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX21 | ENST00000177694.2 | c.326C>G | p.Ala109Gly | missense_variant | 1/6 | 1 | NM_013351.2 | P1 | |
TBX21 | ENST00000581328.1 | n.356C>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000941 AC: 143AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 158AN: 140536Hom.: 1 AF XY: 0.00126 AC XY: 98AN XY: 77592
GnomAD4 exome AF: 0.00122 AC: 1701AN: 1391184Hom.: 2 Cov.: 31 AF XY: 0.00126 AC XY: 866AN XY: 687216
GnomAD4 genome ? AF: 0.000940 AC: 143AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74396
ClinVar
Submissions by phenotype
Asthma, nasal polyps, and aspirin intolerance Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Aug 15, 2019 | TBX21 NM_013351.1 exon1 p.Ala109Gly (c.326C>G): This variant has not been reported in the literature but is present in 0.1% (32/22742) of South Asian alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/17-45811146-C-G). This variant amino acid Glycine (Gly) is present in two species (Black flying fox, Megabat) and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Asthma, nasal polyps, and aspirin intolerance;C5562026:Immunodeficiency 88 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Mar 30, 2021 | TBX21 NM_013351.1 exon1 p.Ala109Gly (c.326C>G): This variant has not been reported in the literature but is present in 0.1% (32/22742) of South Asian alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/17-45811146-C-G). This variant amino acid Glycine (Gly) is present in two species (Black flying fox, Megabat) and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at