22-41436985-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016272.4(TOB2):c.361G>A(p.Gly121Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016272.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TOB2 | NM_016272.4 | c.361G>A | p.Gly121Ser | missense_variant | Exon 2 of 2 | ENST00000327492.4 | NP_057356.1 | |
TOB2 | XM_005261315.3 | c.361G>A | p.Gly121Ser | missense_variant | Exon 2 of 2 | XP_005261372.1 | ||
TOB2 | XM_006724105.4 | c.361G>A | p.Gly121Ser | missense_variant | Exon 2 of 2 | XP_006724168.1 | ||
TOB2 | XM_017028539.2 | c.361G>A | p.Gly121Ser | missense_variant | Exon 2 of 2 | XP_016884028.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251358Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135870
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461890Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 727248
GnomAD4 genome AF: 0.000256 AC: 39AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.361G>A (p.G121S) alteration is located in exon 2 (coding exon 1) of the TOB2 gene. This alteration results from a G to A substitution at nucleotide position 361, causing the glycine (G) at amino acid position 121 to be replaced by a serine (S). 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