X-153785886-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004135.4(IDH3G):c.1168G>A(p.Ala390Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000388 in 1,209,984 control chromosomes in the GnomAD database, including 1 homozygotes. There are 10 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004135.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000888 AC: 1AN: 112672Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34818
GnomAD3 exomes AF: 0.000197 AC: 36AN: 182787Hom.: 0 AF XY: 0.000133 AC XY: 9AN XY: 67431
GnomAD4 exome AF: 0.0000419 AC: 46AN: 1097312Hom.: 1 Cov.: 33 AF XY: 0.0000275 AC XY: 10AN XY: 363148
GnomAD4 genome AF: 0.00000888 AC: 1AN: 112672Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34818
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1168G>A (p.A390T) alteration is located in exon 13 (coding exon 13) of the IDH3G gene. This alteration results from a G to A substitution at nucleotide position 1168, causing the alanine (A) at amino acid position 390 to be replaced by a threonine (T). 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