X-108134368-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_052936.5(ATG4A):āc.424A>Gā(p.Ile142Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,209,945 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_052936.5 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATG4A | NM_052936.5 | c.424A>G | p.Ile142Val | missense_variant | 6/13 | ENST00000372232.8 | NP_443168.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATG4A | ENST00000372232.8 | c.424A>G | p.Ile142Val | missense_variant | 6/13 | 1 | NM_052936.5 | ENSP00000361306.3 |
Frequencies
GnomAD3 genomes AF: 0.00000889 AC: 1AN: 112530Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34674
GnomAD3 exomes AF: 0.00000548 AC: 1AN: 182469Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 66953
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097415Hom.: 0 Cov.: 29 AF XY: 0.00000551 AC XY: 2AN XY: 362825
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112530Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34674
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.424A>G (p.I142V) alteration is located in exon 6 (coding exon 6) of the ATG4A gene. This alteration results from a A to G substitution at nucleotide position 424, causing the isoleucine (I) at amino acid position 142 to be replaced by a valine (V). 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