17-61400404-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_005994.4(TBX2):c.228C>A(p.His76Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00014 in 1,488,184 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 Likely benign (no stars).
Frequency
Consequence
NM_005994.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX2 | NM_005994.4 | c.228C>A | p.His76Gln | missense_variant | Exon 1 of 7 | ENST00000240328.4 | NP_005985.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX2 | ENST00000240328.4 | c.228C>A | p.His76Gln | missense_variant | Exon 1 of 7 | 1 | NM_005994.4 | ENSP00000240328.3 | ||
TBX2 | ENST00000419047.5 | n.228C>A | non_coding_transcript_exon_variant | Exon 1 of 7 | 1 | ENSP00000404781.1 | ||||
TBX2 | ENST00000477081.1 | n.40C>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 2 | |||||
TBX2-AS1 | ENST00000592009.1 | n.41-6657G>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000832 AC: 125AN: 150176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000752 AC: 9AN: 119636Hom.: 0 AF XY: 0.0000454 AC XY: 3AN XY: 66116
GnomAD4 exome AF: 0.0000620 AC: 83AN: 1337900Hom.: 0 Cov.: 32 AF XY: 0.0000530 AC XY: 35AN XY: 660848
GnomAD4 genome AF: 0.000838 AC: 126AN: 150284Hom.: 0 Cov.: 32 AF XY: 0.000764 AC XY: 56AN XY: 73334
ClinVar
Submissions by phenotype
TBX2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at