chr4-73492083-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001133.2(AFM):c.1055C>A(p.Ala352Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000655 in 1,604,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001133.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFM | NM_001133.2 | c.1055C>A | p.Ala352Glu | missense_variant | 8/15 | ENST00000226355.5 | |
AFM | XM_017007842.3 | c.1055C>A | p.Ala352Glu | missense_variant | 8/13 | ||
AFM | XM_017007843.3 | c.1055C>A | p.Ala352Glu | missense_variant | 8/11 | ||
AFM | XM_017007844.3 | c.1055C>A | p.Ala352Glu | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFM | ENST00000226355.5 | c.1055C>A | p.Ala352Glu | missense_variant | 8/15 | 1 | NM_001133.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000368 AC: 56AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000790 AC: 19AN: 240622Hom.: 0 AF XY: 0.0000538 AC XY: 7AN XY: 130176
GnomAD4 exome AF: 0.0000337 AC: 49AN: 1452074Hom.: 0 Cov.: 30 AF XY: 0.0000263 AC XY: 19AN XY: 722434
GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.1055C>A (p.A352E) alteration is located in exon 8 (coding exon 8) of the AFM gene. This alteration results from a C to A substitution at nucleotide position 1055, causing the alanine (A) at amino acid position 352 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at