chrX-30831461-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_152787.5(TAB3):c.2105G>A(p.Arg702His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000679 in 1,208,532 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 22 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152787.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAB3 | NM_152787.5 | c.2105G>A | p.Arg702His | missense_variant | Exon 11 of 11 | ENST00000288422.4 | NP_690000.3 | |
TAB3 | NM_001399872.1 | c.2021G>A | p.Arg674His | missense_variant | Exon 10 of 10 | NP_001386801.1 | ||
TAB3 | NM_001399873.1 | c.2003G>A | p.Arg668His | missense_variant | Exon 10 of 10 | NP_001386802.1 | ||
TAB3 | XM_047441986.1 | c.2105G>A | p.Arg702His | missense_variant | Exon 11 of 11 | XP_047297942.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAB3 | ENST00000288422.4 | c.2105G>A | p.Arg702His | missense_variant | Exon 11 of 11 | 5 | NM_152787.5 | ENSP00000288422.4 | ||
TAB3 | ENST00000378930.7 | c.2105G>A | p.Arg702His | missense_variant | Exon 7 of 7 | 1 | ENSP00000368212.3 | |||
TAB3 | ENST00000378933.5 | c.2105G>A | p.Arg702His | missense_variant | Exon 12 of 12 | 1 | ENSP00000368215.1 | |||
TAB3 | ENST00000378932.6 | c.2021G>A | p.Arg674His | missense_variant | Exon 11 of 11 | 1 | ENSP00000368214.2 |
Frequencies
GnomAD3 genomes AF: 0.000117 AC: 13AN: 111171Hom.: 0 Cov.: 22 AF XY: 0.000120 AC XY: 4AN XY: 33349
GnomAD3 exomes AF: 0.000106 AC: 19AN: 179302Hom.: 0 AF XY: 0.0000618 AC XY: 4AN XY: 64690
GnomAD4 exome AF: 0.0000629 AC: 69AN: 1097309Hom.: 0 Cov.: 30 AF XY: 0.0000496 AC XY: 18AN XY: 362695
GnomAD4 genome AF: 0.000117 AC: 13AN: 111223Hom.: 0 Cov.: 22 AF XY: 0.000120 AC XY: 4AN XY: 33411
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2105G>A (p.R702H) alteration is located in exon 11 (coding exon 7) of the TAB3 gene. This alteration results from a G to A substitution at nucleotide position 2105, causing the arginine (R) at amino acid position 702 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