rs12990669

Positions:

• chr2-3601651-C-G
• chr2-3601651-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024027.5(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 NM_024027.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

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 (HGNC:):

ACMG classification

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
COLEC11	NM_024027.5	c.-26-2664C>G		intron_variant		ENST00000349077.9	NP_076932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLEC11	ENST00000349077.9	c.-26-2664C>G		intron_variant		1	NM_024027.5	ENSP00000339168.4

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9542 AN: 152134 Hom.: 405 Cov.: 33

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

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

Other links and lift over

dbSNP: rs12990669; hg19: chr2-3649241;