chrX-130129641-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004208.4(AIFM1):c.1771-13C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000919 in 1,196,899 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. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004208.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIFM1 | NM_004208.4 | c.1771-13C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000287295.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIFM1 | ENST00000287295.8 | c.1771-13C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004208.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000270 AC: 3AN: 111214Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33394
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 182956Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67486
GnomAD4 exome AF: 0.00000645 AC: 7AN: 1085628Hom.: 0 Cov.: 28 AF XY: 0.00000853 AC XY: 3AN XY: 351594
GnomAD4 genome ? AF: 0.0000359 AC: 4AN: 111271Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33461
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