17-61401842-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_005994.4(TBX2):c.554G>A(p.Arg185His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,612,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005994.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX2 | NM_005994.4 | c.554G>A | p.Arg185His | missense_variant | 2/7 | ENST00000240328.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX2 | ENST00000240328.4 | c.554G>A | p.Arg185His | missense_variant | 2/7 | 1 | NM_005994.4 | P1 | |
TBX2 | ENST00000419047.5 | c.*91G>A | 3_prime_UTR_variant, NMD_transcript_variant | 2/7 | 1 | ||||
TBX2-AS1 | ENST00000592009.1 | n.41-8095C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
TBX2 | ENST00000477081.1 | n.366G>A | non_coding_transcript_exon_variant | 2/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250290Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135724
GnomAD4 exome AF: 0.000203 AC: 297AN: 1460694Hom.: 0 Cov.: 32 AF XY: 0.000187 AC XY: 136AN XY: 726654
GnomAD4 genome AF: 0.000145 AC: 22AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.554G>A (p.R185H) alteration is located in exon 2 (coding exon 2) of the TBX2 gene. This alteration results from a G to A substitution at nucleotide position 554, causing the arginine (R) at amino acid position 185 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at