7-130617016-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012133.6(COPG2):āc.373A>Cā(p.Ile125Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,052 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. I125V) 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>C | p.Ile125Leu | missense_variant | 6/24 | ENST00000425248.5 | |
COPG2 | NM_001290033.2 | c.373A>C | p.Ile125Leu | missense_variant | 6/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COPG2 | ENST00000425248.5 | c.373A>C | p.Ile125Leu | missense_variant | 6/24 | 1 | NM_012133.6 | P1 | |
COPG2 | ENST00000330992.8 | c.373A>C | p.Ile125Leu | missense_variant | 6/20 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459824Hom.: 0 Cov.: 28 AF XY: 0.00000275 AC XY: 2AN XY: 726248
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.373A>C (p.I125L) alteration is located in exon 1 (coding exon 1) of the COPG2 gene. This alteration results from a A to C substitution at nucleotide position 373, causing the isoleucine (I) at amino acid position 125 to be replaced by a leucine (L). 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