2-99018248-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000393483.8(TSGA10):c.2024G>A(p.Arg675His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R675C) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000393483.8 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSGA10 | NM_025244.4 | c.2024G>A | p.Arg675His | missense_variant | 20/21 | ENST00000393483.8 | NP_079520.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSGA10 | ENST00000393483.8 | c.2024G>A | p.Arg675His | missense_variant | 20/21 | 1 | NM_025244.4 | ENSP00000377123.3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151992Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251456Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461734Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727162
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151992Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.2024G>A (p.R675H) alteration is located in exon 20 (coding exon 15) of the TSGA10 gene. This alteration results from a G to A substitution at nucleotide position 2024, causing the arginine (R) at amino acid position 675 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