chr8-119103863-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006438.5(COLEC10):c.410G>A(p.Arg137Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000098 in 1,612,128 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 (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000095 ( 0 hom. )
Consequence
COLEC10
NM_006438.5 missense
NM_006438.5 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 4.32
Genes affected
COLEC10 (HGNC:2220): (collectin subfamily member 10) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.052384347).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC10 | NM_006438.5 | c.410G>A | p.Arg137Gln | missense_variant | 5/6 | ENST00000332843.3 | |
COLEC10 | NM_001324095.2 | c.203G>A | p.Arg68Gln | missense_variant | 7/8 | ||
COLEC10 | XM_005250756.4 | c.203G>A | p.Arg68Gln | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC10 | ENST00000332843.3 | c.410G>A | p.Arg137Gln | missense_variant | 5/6 | 1 | NM_006438.5 | P1 | |
COLEC10 | ENST00000521788.1 | n.666G>A | non_coding_transcript_exon_variant | 7/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000132 AC: 20AN: 152062Hom.: 0 Cov.: 32
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?
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GnomAD3 exomes AF: 0.000136 AC: 34AN: 250698Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135504
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GnomAD4 exome AF: 0.0000945 AC: 138AN: 1459948Hom.: 0 Cov.: 29 AF XY: 0.000100 AC XY: 73AN XY: 726396
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GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74382
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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 | Apr 27, 2022 | The c.410G>A (p.R137Q) alteration is located in exon 5 (coding exon 5) of the COLEC10 gene. This alteration results from a G to A substitution at nucleotide position 410, causing the arginine (R) at amino acid position 137 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
Uncertain
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Uncertain
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Uncertain
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