18-12329565-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_006796.3(AFG3L2):āc.2394G>Cā(p.Ter798Tyrext*?) variant causes a stop lost change. The variant allele was found at a frequency of 0.000031 in 1,613,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_006796.3 stop_lost
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AFG3L2 | NM_006796.3 | c.2394G>C | p.Ter798Tyrext*? | stop_lost | Exon 17 of 17 | ENST00000269143.8 | NP_006787.2 | |
AFG3L2 | XM_011525601.4 | c.2193G>C | p.Ter731Tyrext*? | stop_lost | Exon 16 of 16 | XP_011523903.1 | ||
TUBB6 | NM_001303525.2 | c.*382C>G | 3_prime_UTR_variant | Exon 4 of 4 | NP_001290454.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251466Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135908
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461490Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727016
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74476
ClinVar
Submissions by phenotype
Spastic ataxia 5 Uncertain:1
The stop lost p.*798Yext*32 in AFG3L2 (NM_006796.3) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.*798Yext*32 variant is observed in 26/30,616 (0.0849%) alleles from individuals of South Asian background in gnomAD Exomes. The nucleotide c.2394 in AFG3L2 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. -
not provided Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at