2-119157926-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_182528.4(C1QL2):c.344G>A(p.Gly115Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000064 in 1,546,528 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182528.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1QL2 | NM_182528.4 | c.344G>A | p.Gly115Glu | missense_variant | Exon 1 of 2 | ENST00000272520.4 | NP_872334.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000347 AC: 5AN: 144200Hom.: 0 AF XY: 0.0000256 AC XY: 2AN XY: 78260
GnomAD4 exome AF: 0.0000624 AC: 87AN: 1394388Hom.: 0 Cov.: 37 AF XY: 0.0000553 AC XY: 38AN XY: 687750
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152140Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.344G>A (p.G115E) alteration is located in exon 1 (coding exon 1) of the C1QL2 gene. This alteration results from a G to A substitution at nucleotide position 344, causing the glycine (G) at amino acid position 115 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