7-130617016-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012133.6(COPG2):āc.373A>Gā(p.Ile125Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,052 control chromosomes in the GnomAD database, with no homozygous occurrence. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I125L) has been classified as Uncertain significance.
Frequency
Consequence
NM_012133.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COPG2 | NM_012133.6 | c.373A>G | p.Ile125Val | missense_variant | 6/24 | ENST00000425248.5 | |
COPG2 | NM_001290033.2 | c.373A>G | p.Ile125Val | missense_variant | 6/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COPG2 | ENST00000425248.5 | c.373A>G | p.Ile125Val | missense_variant | 6/24 | 1 | NM_012133.6 | P1 | |
COPG2 | ENST00000330992.8 | c.373A>G | p.Ile125Val | missense_variant | 6/20 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248206Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134678
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459824Hom.: 0 Cov.: 28 AF XY: 0.00000413 AC XY: 3AN XY: 726248
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.373A>G (p.I125V) alteration is located in exon 1 (coding exon 1) of the COPG2 gene. This alteration results from a A to G substitution at nucleotide position 373, causing the isoleucine (I) at amino acid position 125 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