chr17-47733844-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_013351.2(TBX21):c.390A>G(p.Gly130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,609,696 control chromosomes in the GnomAD database, including 62,161 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.28 ( 6253 hom., cov: 32)
Exomes 𝑓: 0.27 ( 55908 hom. )
Consequence
TBX21
NM_013351.2 synonymous
NM_013351.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.469
Genes affected
TBX21 (HGNC:11599): (T-box transcription factor 21) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene is the human ortholog of mouse Tbx21/Tbet gene. Studies in mouse show that Tbx21 protein is a Th1 cell-specific transcription factor that controls the expression of the hallmark Th1 cytokine, interferon-gamma (IFNG). Expression of the human ortholog also correlates with IFNG expression in Th1 and natural killer cells, suggesting a role for this gene in initiating Th1 lineage development from naive Th precursor cells. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 17-47733844-A-G is Benign according to our data. Variant chr17-47733844-A-G is described in ClinVar as [Benign]. Clinvar id is 1334938.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-47733844-A-G is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=0.469 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX21 | NM_013351.2 | c.390A>G | p.Gly130= | synonymous_variant | 1/6 | ENST00000177694.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX21 | ENST00000177694.2 | c.390A>G | p.Gly130= | synonymous_variant | 1/6 | 1 | NM_013351.2 | P1 | |
TBX21 | ENST00000581328.1 | n.420A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.282 AC: 42789AN: 151746Hom.: 6257 Cov.: 32
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GnomAD3 exomes AF: 0.296 AC: 70657AN: 238706Hom.: 11079 AF XY: 0.298 AC XY: 38918AN XY: 130754
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GnomAD4 exome AF: 0.272 AC: 395860AN: 1457832Hom.: 55908 Cov.: 35 AF XY: 0.274 AC XY: 198834AN XY: 725092
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GnomAD4 genome AF: 0.282 AC: 42805AN: 151864Hom.: 6253 Cov.: 32 AF XY: 0.284 AC XY: 21118AN XY: 74242
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 47% of patients studied by a panel of primary immunodeficiencies. Number of patients: 45. Only high quality variants are reported. - |
Immunodeficiency 88 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at