8-119106116-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_006438.5(COLEC10):c.759C>T(p.Ser253=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,824 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000062 ( 1 hom. )
Consequence
COLEC10
NM_006438.5 synonymous
NM_006438.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.426
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 -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
?
Variant 8-119106116-C-T is Benign according to our data. Variant chr8-119106116-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1695236.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.426 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC10 | NM_006438.5 | c.759C>T | p.Ser253= | synonymous_variant | 6/6 | ENST00000332843.3 | |
COLEC10 | NM_001324095.2 | c.552C>T | p.Ser184= | synonymous_variant | 8/8 | ||
COLEC10 | XM_005250756.4 | c.552C>T | p.Ser184= | synonymous_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC10 | ENST00000332843.3 | c.759C>T | p.Ser253= | synonymous_variant | 6/6 | 1 | NM_006438.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152172Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000136 AC: 34AN: 250764Hom.: 1 AF XY: 0.000170 AC XY: 23AN XY: 135488
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GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461534Hom.: 1 Cov.: 31 AF XY: 0.0000990 AC XY: 72AN XY: 727068
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74466
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
COLEC10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 06, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | COLEC10: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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