rs75743672
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_005994.4(TBX2):c.366C>A(p.Gly122Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0734 in 1,577,446 control chromosomes in the GnomAD database, including 6,201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005994.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX2 | NM_005994.4 | c.366C>A | p.Gly122Gly | synonymous_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.366C>A | p.Gly122Gly | synonymous_variant | Exon 1 of 7 | 1 | NM_005994.4 | ENSP00000240328.3 | ||
TBX2 | ENST00000419047.5 | n.366C>A | non_coding_transcript_exon_variant | Exon 1 of 7 | 1 | ENSP00000404781.1 | ||||
TBX2 | ENST00000477081.1 | n.178C>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 2 | |||||
TBX2-AS1 | ENST00000592009.1 | n.41-6795G>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0928 AC: 14095AN: 151816Hom.: 902 Cov.: 32
GnomAD3 exomes AF: 0.115 AC: 21498AN: 187362Hom.: 1812 AF XY: 0.110 AC XY: 11085AN XY: 100982
GnomAD4 exome AF: 0.0713 AC: 101701AN: 1425522Hom.: 5291 Cov.: 34 AF XY: 0.0725 AC XY: 51140AN XY: 705512
GnomAD4 genome AF: 0.0930 AC: 14128AN: 151924Hom.: 910 Cov.: 32 AF XY: 0.0982 AC XY: 7291AN XY: 74238
ClinVar
Submissions by phenotype
not provided Benign:2
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TBX2-related disorder Benign:1
This variant is classified as 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