chrX-130165585-G-A
Variant summary
Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_004208.4(AIFM1):c.72C>T(p.Cys24Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000673 in 1,199,365 control chromosomes in the GnomAD database, including 2 homozygotes. There are 234 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 synonymous
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AIFM1 | NM_004208.4 | c.72C>T | p.Cys24Cys | synonymous_variant | Exon 1 of 16 | ENST00000287295.8 | NP_004199.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AIFM1 | ENST00000287295.8 | c.72C>T | p.Cys24Cys | synonymous_variant | Exon 1 of 16 | 1 | NM_004208.4 | ENSP00000287295.3 | ||
AIFM1 | ENST00000675092.1 | c.72C>T | p.Cys24Cys | synonymous_variant | Exon 1 of 16 | ENSP00000501772.1 |
Frequencies
GnomAD3 genomes AF: 0.000489 AC: 55AN: 112526Hom.: 0 Cov.: 24 show subpopulations
GnomAD2 exomes AF: 0.000301 AC: 47AN: 156137 AF XY: 0.000325 show subpopulations
GnomAD4 exome AF: 0.000692 AC: 752AN: 1086786Hom.: 2 Cov.: 30 AF XY: 0.000619 AC XY: 220AN XY: 355588 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000489 AC: 55AN: 112579Hom.: 0 Cov.: 24 AF XY: 0.000403 AC XY: 14AN XY: 34765 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:6
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AIFM1: BP4, BP7, BS2 -
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Charcot-Marie-Tooth disease Benign:1
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Severe X-linked mitochondrial encephalomyopathy Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Combined oxidative phosphorylation deficiency;CN118851:Charcot-Marie-Tooth Neuropathy X Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at