chr5-175968045-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032361.4(THOC3):c.164G>A(p.Ser55Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000262 in 152,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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: 0.0000263 AC: 4AN: 152284Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000135 AC: 33AN: 245106Hom.: 0 AF XY: 0.0000969 AC XY: 13AN XY: 134142
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000274 AC: 40AN: 1459188Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 725910
GnomAD4 genome AF: 0.0000262 AC: 4AN: 152402Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74526
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.164G>A (p.S55N) alteration is located in exon 1 (coding exon 1) of the THOC3 gene. This alteration results from a G to A substitution at nucleotide position 164, causing the serine (S) at amino acid position 55 to be replaced by an asparagine (N). 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