chrX-130156540-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_004208.4(AIFM1):āc.170C>Gā(p.Ser57Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000067 in 1,209,790 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 35 hemizygotes in GnomAD. 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_004208.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIFM1 | NM_004208.4 | c.170C>G | p.Ser57Cys | missense_variant | 2/16 | ENST00000287295.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIFM1 | ENST00000287295.8 | c.170C>G | p.Ser57Cys | missense_variant | 2/16 | 1 | NM_004208.4 |
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 12AN: 111862Hom.: 0 Cov.: 23 AF XY: 0.000147 AC XY: 5AN XY: 34026
GnomAD3 exomes AF: 0.0000599 AC: 11AN: 183496Hom.: 0 AF XY: 0.0000589 AC XY: 4AN XY: 67934
GnomAD4 exome AF: 0.0000628 AC: 69AN: 1097928Hom.: 0 Cov.: 30 AF XY: 0.0000826 AC XY: 30AN XY: 363296
GnomAD4 genome AF: 0.000107 AC: 12AN: 111862Hom.: 0 Cov.: 23 AF XY: 0.000147 AC XY: 5AN XY: 34026
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 23, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 12, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 04, 2020 | See Variant Classification Assertion Criteria. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 14, 2015 | Lines of evidence used in support of classification: UNCERTAIN: Alteration(s) of Uncertain Clinical Significance Detected - |
Charcot-Marie-Tooth disease X-linked recessive 4;C1845095:Deafness, X-linked 5;C3151753:Severe X-linked mitochondrial encephalomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Combined oxidative phosphorylation deficiency;CN118851:Charcot-Marie-Tooth Neuropathy X Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at