rs12990669

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000349077.9(COLEC11):​c.-26-2664C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 152,252 control chromosomes in the GnomAD database, including 406 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.063 ( 406 hom., cov: 33)

Consequence

COLEC11
ENST00000349077.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0899 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COLEC11NM_024027.5 linkuse as main transcriptc.-26-2664C>G intron_variant ENST00000349077.9 NP_076932.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COLEC11ENST00000349077.9 linkuse as main transcriptc.-26-2664C>G intron_variant 1 NM_024027.5 ENSP00000339168 P1Q9BWP8-1

Frequencies

GnomAD3 genomes
AF:
0.0627
AC:
9542
AN:
152134
Hom.:
405
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0174
Gnomad AMI
AF:
0.107
Gnomad AMR
AF:
0.0624
Gnomad ASJ
AF:
0.0910
Gnomad EAS
AF:
0.0423
Gnomad SAS
AF:
0.0801
Gnomad FIN
AF:
0.0386
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.0919
Gnomad OTH
AF:
0.0777
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0626
AC:
9537
AN:
152252
Hom.:
406
Cov.:
33
AF XY:
0.0602
AC XY:
4484
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0174
Gnomad4 AMR
AF:
0.0623
Gnomad4 ASJ
AF:
0.0910
Gnomad4 EAS
AF:
0.0424
Gnomad4 SAS
AF:
0.0804
Gnomad4 FIN
AF:
0.0386
Gnomad4 NFE
AF:
0.0918
Gnomad4 OTH
AF:
0.0769
Alfa
AF:
0.0235
Hom.:
23
Bravo
AF:
0.0614
Asia WGS
AF:
0.0700
AC:
244
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.4
DANN
Benign
0.35

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: rs12990669; hg19: chr2-3649241; API