X-153785958-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004135.4(IDH3G):āc.1096A>Gā(p.Ile366Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,209,693 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 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 (ā ).
Frequency
Consequence
NM_004135.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000889 AC: 1AN: 112458Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34614
GnomAD3 exomes AF: 0.0000219 AC: 4AN: 182760Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67556
GnomAD4 exome AF: 0.00000729 AC: 8AN: 1097235Hom.: 0 Cov.: 33 AF XY: 0.00000551 AC XY: 2AN XY: 363067
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112458Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34614
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1096A>G (p.I366V) alteration is located in exon 13 (coding exon 13) of the IDH3G gene. This alteration results from a A to G substitution at nucleotide position 1096, causing the isoleucine (I) at amino acid position 366 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