chr18-346549-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130386.3(COLEC12):c.1073G>A(p.Arg358Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,614,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R358P) has been classified as Uncertain significance.
Frequency
Consequence
NM_130386.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC12 | NM_130386.3 | c.1073G>A | p.Arg358Gln | missense_variant | 5/10 | ENST00000400256.5 | |
COLEC12 | XM_011525741.3 | c.1022G>A | p.Arg341Gln | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC12 | ENST00000400256.5 | c.1073G>A | p.Arg358Gln | missense_variant | 5/10 | 1 | NM_130386.3 | P1 | |
COLEC12 | ENST00000582147.1 | n.1281G>A | non_coding_transcript_exon_variant | 5/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251442Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135900
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461868Hom.: 0 Cov.: 33 AF XY: 0.0000509 AC XY: 37AN XY: 727240
GnomAD4 genome AF: 0.000171 AC: 26AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.1073G>A (p.R358Q) alteration is located in exon 5 (coding exon 5) of the COLEC12 gene. This alteration results from a G to A substitution at nucleotide position 1073, causing the arginine (R) at amino acid position 358 to be replaced by a glutamine (Q). 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