18-335075-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130386.3(COLEC12):āc.1483G>Cā(p.Glu495Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000745 in 1,611,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00019 ( 0 hom., cov: 32)
Exomes š: 0.000062 ( 0 hom. )
Consequence
COLEC12
NM_130386.3 missense
NM_130386.3 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 4.00
Genes affected
COLEC12 (HGNC:16016): (collectin subfamily member 12) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. This protein is a scavenger receptor that displays several functions associated with host defense. It can bind to carbohydrate antigens on microorganisms, facilitating their recognition and removal. It also mediates the recognition, internalization, and degradation of oxidatively modified low density lipoprotein by vascular endothelial cells. [provided by RefSeq, May 2018]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12056044).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COLEC12 | NM_130386.3 | c.1483G>C | p.Glu495Gln | missense_variant | 6/10 | ENST00000400256.5 | NP_569057.2 | |
COLEC12 | XM_011525741.3 | c.1432G>C | p.Glu478Gln | missense_variant | 5/9 | XP_011524043.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COLEC12 | ENST00000400256.5 | c.1483G>C | p.Glu495Gln | missense_variant | 6/10 | 1 | NM_130386.3 | ENSP00000383115 | P1 | |
COLEC12 | ENST00000582147.1 | n.1691G>C | non_coding_transcript_exon_variant | 6/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 151952Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000774 AC: 19AN: 245420Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133740
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GnomAD4 exome AF: 0.0000624 AC: 91AN: 1459060Hom.: 0 Cov.: 36 AF XY: 0.0000606 AC XY: 44AN XY: 725920
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GnomAD4 genome AF: 0.000191 AC: 29AN: 151952Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74206
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2022 | The c.1483G>C (p.E495Q) alteration is located in exon 6 (coding exon 6) of the COLEC12 gene. This alteration results from a G to C substitution at nucleotide position 1483, causing the glutamic acid (E) at amino acid position 495 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at