rs7567833

Variant names:

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1

The NM_024027.5(COLEC11):c.656A>G(p.His219Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0685 in 1,613,746 control chromosomes in the GnomAD database, including 19,382 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.22 ( 9520 hom., cov: 34)

Exomes 𝑓: 0.053 ( 9862 hom. )

Consequence

COLEC11
NM_024027.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.72

Variant links:

Genes affected

COLEC11 (HGNC:17213): (collectin subfamily member 11) This gene encodes a member of the collectin family of C-type lectins that possess collagen-like sequences and carbohydrate recognition domains. Collectins are secreted proteins that play important roles in the innate immune system by binding to carbohydrate antigens on microorganisms, facilitating their recognition and removal. The encoded protein binds to multiple sugars with a preference for fucose and mannose. Mutations in this gene are a cause of 3MC syndrome-2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

COLEC11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM1

In a domain C-type lectin (size 116) in uniprot entity COL11_HUMAN there are 6 pathogenic changes around while only 2 benign (75%) in NM_024027.5

BP4

Computational evidence support a benign effect (MetaRNN=7.5731377E-6).

BP6

Variant 2-3643958-A-G is Benign according to our data. Variant chr2-3643958-A-G is described in ClinVar as [Benign]. Clinvar id is 1588878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC11	NM_024027.5 link	c.656A>G	p.His219Arg	missense_variant	Exon 7 of 7	ENST00000349077.9	NP_076932.1	Q9BWP8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC11	ENST00000349077.9 link	c.656A>G	p.His219Arg	missense_variant	Exon 7 of 7	1	NM_024027.5	ENSP00000339168.4		Q9BWP8-1

Frequencies

GnomAD3 genomes

AF:

0.215

AC:

32710

AN:

151850

Hom.:

9482

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.0922

Gnomad ASJ

AF:

0.0386

Gnomad EAS

AF:

0.0213

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0167

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.0336

Gnomad OTH

AF:

0.188

GnomAD3 exomes

AF:

0.0845

AC:

21235

AN:

251312

Hom.:

4159

AF XY:

0.0749

AC XY:

10176

AN XY:

135868

show subpopulations

Gnomad AFR exome

AF:

0.685

Gnomad AMR exome

AF:

0.0485

Gnomad ASJ exome

AF:

0.0367

Gnomad EAS exome

AF:

0.0171

Gnomad SAS exome

AF:

0.103

Gnomad FIN exome

AF:

0.0186

Gnomad NFE exome

AF:

0.0339

Gnomad OTH exome

AF:

0.0592

GnomAD4 exome

AF:

0.0531

AC:

77681

AN:

1461780

Hom.:

9862

Cov.:

AF XY:

0.0528

AC XY:

38427

AN XY:

727196

show subpopulations

Gnomad4 AFR exome

AF:

0.692

Gnomad4 AMR exome

AF:

0.0540

Gnomad4 ASJ exome

AF:

0.0375

Gnomad4 EAS exome

AF:

0.0181

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.0193

Gnomad4 NFE exome

AF:

0.0313

Gnomad4 OTH exome

AF:

0.0811

GnomAD4 genome

AF:

0.216

AC:

32804

AN:

151966

Hom.:

9520

Cov.:

AF XY:

0.210

AC XY:

15594

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.667

Gnomad4 AMR

AF:

0.0921

Gnomad4 ASJ

AF:

0.0386

Gnomad4 EAS

AF:

0.0214

Gnomad4 SAS

AF:

0.110

Gnomad4 FIN

AF:

0.0167

Gnomad4 NFE

AF:

0.0336

Gnomad4 OTH

AF:

0.187

Alfa

AF:

0.0684

Hom.:

4170

Bravo

AF:

0.239

TwinsUK

AF:

0.0324

AC:

120

ALSPAC

AF:

0.0304

AC:

117

ESP6500AA

AF:

0.660

AC:

2910

ESP6500EA

AF:

0.0324

AC:

279

ExAC

AF:

0.0987

AC:

11983

Asia WGS

AF:

0.107

AC:

376

AN:

3478

EpiCase

AF:

0.0351

EpiControl

AF:

0.0359

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.046

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.83

DEOGEN2

Benign

0.0065

.;.;T;.;.;.;.;.

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.45

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.34

T;T;T;T;T;T;T;T

MetaRNN

Benign

0.0000076

T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.89

.;.;N;.;.;.;.;.

PrimateAI

Uncertain

0.50

PROVEAN

Benign

0.13

N;N;N;N;N;N;N;N

REVEL

Benign

0.14

Sift

Benign

0.48

T;T;T;T;T;T;T;T

Sift4G

Benign

0.62

T;T;T;T;T;T;T;T

Polyphen

0.0

B;B;B;.;B;B;B;B

Vest4

0.11

MPC

0.47

ClinPred

0.0040

GERP RS

5.3

Varity_R

0.25

gMVP

0.54

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over