1-62819021-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032852.4(ATG4C):c.411T>G(p.Asp137Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,412,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032852.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATG4C | NM_032852.4 | c.411T>G | p.Asp137Glu | missense_variant | 5/11 | ENST00000317868.9 | |
ATG4C | NM_178221.3 | c.411T>G | p.Asp137Glu | missense_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATG4C | ENST00000317868.9 | c.411T>G | p.Asp137Glu | missense_variant | 5/11 | 1 | NM_032852.4 | P1 | |
ATG4C | ENST00000371120.7 | c.411T>G | p.Asp137Glu | missense_variant | 5/11 | 1 | P1 | ||
ATG4C | ENST00000371118.1 | c.411T>G | p.Asp137Glu | missense_variant | 5/5 | 5 | |||
ATG4C | ENST00000443289.5 | c.411T>G | p.Asp137Glu | missense_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000170 AC: 24AN: 1412898Hom.: 0 Cov.: 31 AF XY: 0.0000158 AC XY: 11AN XY: 698144
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.411T>G (p.D137E) alteration is located in exon 5 (coding exon 4) of the ATG4C gene. This alteration results from a T to G substitution at nucleotide position 411, causing the aspartic acid (D) at amino acid position 137 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