18-12340315-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_006796.3(AFG3L2):c.1866G>A(p.Leu622Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,916 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006796.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AFG3L2 | NM_006796.3 | c.1866G>A | p.Leu622Leu | synonymous_variant | Exon 15 of 17 | ENST00000269143.8 | NP_006787.2 | |
AFG3L2 | XM_011525601.4 | c.1780-2780G>A | intron_variant | Intron 14 of 15 | XP_011523903.1 | |||
LOC107985154 | XR_001753363.2 | n.781+1735C>T | intron_variant | Intron 1 of 1 | ||||
LOC107985154 | XR_002958227.2 | n.3291+3413C>T | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251484Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135918
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461748Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727188
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74332
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown -
- -
not specified Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at