chr8-119103843-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_006438.5(COLEC10):āc.390A>Gā(p.Gln130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00659 in 1,612,898 control chromosomes in the GnomAD database, including 562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.034 ( 273 hom., cov: 32)
Exomes š: 0.0038 ( 289 hom. )
Consequence
COLEC10
NM_006438.5 synonymous
NM_006438.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.342
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 Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 8-119103843-A-G is Benign according to our data. Variant chr8-119103843-A-G is described in ClinVar as [Benign]. Clinvar id is 3055343.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.342 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC10 | NM_006438.5 | c.390A>G | p.Gln130= | synonymous_variant | 5/6 | ENST00000332843.3 | |
COLEC10 | NM_001324095.2 | c.183A>G | p.Gln61= | synonymous_variant | 7/8 | ||
COLEC10 | XM_005250756.4 | c.183A>G | p.Gln61= | synonymous_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC10 | ENST00000332843.3 | c.390A>G | p.Gln130= | synonymous_variant | 5/6 | 1 | NM_006438.5 | P1 | |
COLEC10 | ENST00000521788.1 | n.646A>G | non_coding_transcript_exon_variant | 7/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0336 AC: 5112AN: 152130Hom.: 273 Cov.: 32
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GnomAD3 exomes AF: 0.00879 AC: 2205AN: 250890Hom.: 114 AF XY: 0.00665 AC XY: 902AN XY: 135606
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GnomAD4 exome AF: 0.00378 AC: 5518AN: 1460650Hom.: 289 Cov.: 29 AF XY: 0.00331 AC XY: 2406AN XY: 726692
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GnomAD4 genome AF: 0.0336 AC: 5116AN: 152248Hom.: 273 Cov.: 32 AF XY: 0.0326 AC XY: 2427AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
COLEC10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at