5-82164426-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031482.5(ATG10):āc.244T>Cā(p.Cys82Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,020 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 (ā ).
Frequency
Consequence
NM_031482.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATG10 | NM_031482.5 | c.244T>C | p.Cys82Arg | missense_variant | 4/8 | ENST00000282185.8 | NP_113670.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATG10 | ENST00000282185.8 | c.244T>C | p.Cys82Arg | missense_variant | 4/8 | 1 | NM_031482.5 | ENSP00000282185 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251114Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135698
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461746Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727156
GnomAD4 genome AF: 0.000190 AC: 29AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.244T>C (p.C82R) alteration is located in exon 5 (coding exon 3) of the ATG10 gene. This alteration results from a T to C substitution at nucleotide position 244, causing the cysteine (C) at amino acid position 82 to be replaced by an arginine (R). 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