chrX-123621158-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001081550.2(THOC2):c.4215G>A(p.Arg1405=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.0000403 in 1,192,106 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001081550.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THOC2 | NM_001081550.2 | c.4215G>A | p.Arg1405= | splice_region_variant, synonymous_variant | 31/39 | ENST00000245838.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THOC2 | ENST00000245838.13 | c.4215G>A | p.Arg1405= | splice_region_variant, synonymous_variant | 31/39 | 5 | NM_001081550.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000629 AC: 7AN: 111292Hom.: 0 Cov.: 22 AF XY: 0.0000596 AC XY: 2AN XY: 33536
GnomAD3 exomes AF: 0.0000307 AC: 5AN: 162734Hom.: 0 AF XY: 0.0000364 AC XY: 2AN XY: 54928
GnomAD4 exome AF: 0.0000379 AC: 41AN: 1080814Hom.: 0 Cov.: 30 AF XY: 0.0000453 AC XY: 16AN XY: 353272
GnomAD4 genome AF: 0.0000629 AC: 7AN: 111292Hom.: 0 Cov.: 22 AF XY: 0.0000596 AC XY: 2AN XY: 33536
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at