chr8-119105892-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006438.5(COLEC10):c.535C>T(p.Arg179Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000365 in 1,613,770 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0016 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 1 hom. )
Consequence
COLEC10
NM_006438.5 missense
NM_006438.5 missense
Scores
5
8
6
Clinical Significance
Conservation
PhyloP100: 2.77
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 -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.02266121).
BP6
?
Variant 8-119105892-C-T is Benign according to our data. Variant chr8-119105892-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 709347.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC10 | NM_006438.5 | c.535C>T | p.Arg179Trp | missense_variant | 6/6 | ENST00000332843.3 | |
COLEC10 | NM_001324095.2 | c.328C>T | p.Arg110Trp | missense_variant | 8/8 | ||
COLEC10 | XM_005250756.4 | c.328C>T | p.Arg110Trp | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC10 | ENST00000332843.3 | c.535C>T | p.Arg179Trp | missense_variant | 6/6 | 1 | NM_006438.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00156 AC: 238AN: 152090Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000523 AC: 131AN: 250616Hom.: 1 AF XY: 0.000451 AC XY: 61AN XY: 135394
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GnomAD4 exome AF: 0.000240 AC: 351AN: 1461562Hom.: 1 Cov.: 31 AF XY: 0.000272 AC XY: 198AN XY: 727076
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GnomAD4 genome ? AF: 0.00156 AC: 238AN: 152208Hom.: 1 Cov.: 32 AF XY: 0.00171 AC XY: 127AN XY: 74424
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
T
Polyphen
D
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