chr17-47733553-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013351.2(TBX21):c.99C>G(p.His33Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 1,487,136 control chromosomes in the GnomAD database, including 1,068 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_013351.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX21 | NM_013351.2 | c.99C>G | p.His33Gln | missense_variant | 1/6 | ENST00000177694.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX21 | ENST00000177694.2 | c.99C>G | p.His33Gln | missense_variant | 1/6 | 1 | NM_013351.2 | P1 | |
TBX21 | ENST00000581328.1 | n.129C>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0301 AC: 4577AN: 152020Hom.: 156 Cov.: 32
GnomAD3 exomes AF: 0.0488 AC: 4004AN: 82008Hom.: 164 AF XY: 0.0474 AC XY: 2231AN XY: 47062
GnomAD4 exome AF: 0.0309 AC: 41282AN: 1335008Hom.: 911 Cov.: 31 AF XY: 0.0317 AC XY: 20884AN XY: 658392
GnomAD4 genome AF: 0.0302 AC: 4588AN: 152128Hom.: 157 Cov.: 32 AF XY: 0.0315 AC XY: 2343AN XY: 74366
ClinVar
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 22% of patients studied by a panel of primary immunodeficiencies. Number of patients: 21. Only high quality variants are reported. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at