X-130129963-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004208.4(AIFM1):c.1770+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,209,543 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004208.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIFM1 | NM_004208.4 | c.1770+7G>T | splice_region_variant, intron_variant | ENST00000287295.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIFM1 | ENST00000287295.8 | c.1770+7G>T | splice_region_variant, intron_variant | 1 | NM_004208.4 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 112096Hom.: 0 Cov.: 22 AF XY: 0.0000292 AC XY: 1AN XY: 34250
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183008Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67542
GnomAD4 exome AF: 0.0000200 AC: 22AN: 1097447Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 3AN XY: 362809
GnomAD4 genome AF: 0.0000268 AC: 3AN: 112096Hom.: 0 Cov.: 22 AF XY: 0.0000292 AC XY: 1AN XY: 34250
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation deficiency;CN118851:Charcot-Marie-Tooth Neuropathy X Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at