5-175968153-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032361.4(THOC3):c.56G>T(p.Gly19Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 152,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032361.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152306Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000174 AC: 4AN: 230482Hom.: 0 AF XY: 0.00000788 AC XY: 1AN XY: 126932
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000117 AC: 17AN: 1452940Hom.: 0 Cov.: 33 AF XY: 0.00000969 AC XY: 7AN XY: 722274
GnomAD4 genome AF: 0.000105 AC: 16AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.56G>T (p.G19V) alteration is located in exon 1 (coding exon 1) of the THOC3 gene. This alteration results from a G to T substitution at nucleotide position 56, causing the glycine (G) at amino acid position 19 to be replaced by a valine (V). 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