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GeneBe

8-119103843-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_006438.5(COLEC10):c.390A>G(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 (★).

Frequency

Genomes: 𝑓 0.034 ( 273 hom., cov: 32)
Exomes 𝑓: 0.0038 ( 289 hom. )

Consequence

COLEC10
NM_006438.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.342
Variant links:
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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.342 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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
COLEC10NM_006438.5 linkuse as main transcriptc.390A>G p.Gln130= synonymous_variant 5/6 ENST00000332843.3
COLEC10NM_001324095.2 linkuse as main transcriptc.183A>G p.Gln61= synonymous_variant 7/8
COLEC10XM_005250756.4 linkuse as main transcriptc.183A>G p.Gln61= synonymous_variant 5/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COLEC10ENST00000332843.3 linkuse as main transcriptc.390A>G p.Gln130= synonymous_variant 5/61 NM_006438.5 P1
COLEC10ENST00000521788.1 linkuse as main transcriptn.646A>G non_coding_transcript_exon_variant 7/73

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0336
AC:
5112
AN:
152130
Hom.:
273
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.116
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0143
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000500
Gnomad OTH
AF:
0.0263
GnomAD3 exomes
AF:
0.00879
AC:
2205
AN:
250890
Hom.:
114
AF XY:
0.00665
AC XY:
902
AN XY:
135606
show subpopulations
Gnomad AFR exome
AF:
0.117
Gnomad AMR exome
AF:
0.00638
Gnomad ASJ exome
AF:
0.000695
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000360
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000317
Gnomad OTH exome
AF:
0.00605
GnomAD4 exome
AF:
0.00378
AC:
5518
AN:
1460650
Hom.:
289
Cov.:
29
AF XY:
0.00331
AC XY:
2406
AN XY:
726692
show subpopulations
Gnomad4 AFR exome
AF:
0.129
Gnomad4 AMR exome
AF:
0.00696
Gnomad4 ASJ exome
AF:
0.000728
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000336
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000198
Gnomad4 OTH exome
AF:
0.00966
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0336
AC:
5116
AN:
152248
Hom.:
273
Cov.:
32
AF XY:
0.0326
AC XY:
2427
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.116
Gnomad4 AMR
AF:
0.0142
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000500
Gnomad4 OTH
AF:
0.0260
Alfa
AF:
0.00802
Hom.:
100
Bravo
AF:
0.0391
Asia WGS
AF:
0.00722
AC:
25
AN:
3478
EpiCase
AF:
0.000655
EpiControl
AF:
0.000771

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 submitterclinical testingPreventionGenetics, part of Exact SciencesMar 08, 2019This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
Cadd
Benign
5.4
Dann
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34834488; hg19: chr8-120116082; API