chr2-3594771-T-C

Variant names:

• chr2-3594771-T-C
• rs3820897
• ENST00000382062.6:c.-424T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000382062.6(COLEC11):​c.-424T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 215,862 control chromosomes in the GnomAD database, including 68,465 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 0.80 (50472 hom., cov: 32)
  • Exomes 𝑓: 0.73 (17993 hom.)
• Consequence: COLEC11 ENST00000382062.6 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 23 publications found

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 Gene-Disease associations (from GenCC):

• 3MC syndrome 2

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
• 3MC syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000382062.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC11	ENST00000382062.6	TSL:1	c.-424T>C		upstream_gene	N/A	ENSP00000371494.2
	COLEC11	ENST00000460971.5	TSL:1	n.-184T>C		upstream_gene	N/A
	COLEC11	ENST00000487365.5	TSL:1	n.-184T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121917 AN: 152034 Hom.: 50427 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.819

GnomAD4 exome AF: 0.734 AC: 46765 AN: 63708 Hom.: 17993 AF XY: 0.708 AC XY: 24917 AN XY: 35206

African (AFR) AF: 0.926 AC: 893 AN: 964

American (AMR) AF: 0.752 AC: 1556 AN: 2068

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 1158 AN: 1364

East Asian (EAS) AF: 0.263 AC: 283 AN: 1078

South Asian (SAS) AF: 0.553 AC: 7855 AN: 14208

European-Finnish (FIN) AF: 0.643 AC: 3020 AN: 4694

Middle Eastern (MID) AF: 0.827 AC: 187 AN: 226

European-Non Finnish (NFE) AF: 0.818 AC: 29339 AN: 35852

Other (OTH) AF: 0.760 AC: 2474 AN: 3254

GnomAD4 genome AF: 0.802 AC: 122014 AN: 152154 Hom.: 50472 Cov.: 32 AF XY: 0.784 AC XY: 58282 AN XY: 74374

African (AFR) AF: 0.930 AC: 38641 AN: 41548

American (AMR) AF: 0.773 AC: 11812 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2901 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1396 AN: 5160

South Asian (SAS) AF: 0.534 AC: 2575 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6576 AN: 10544

Middle Eastern (MID) AF: 0.842 AC: 246 AN: 292

European-Non Finnish (NFE) AF: 0.814 AC: 55349 AN: 68008

Other (OTH) AF: 0.811 AC: 1714 AN: 2114

Alfa AF: 0.808 Hom.: 190477

Bravo AF: 0.820

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.1
DANN	Benign	0.43
PhyloP100		0.33
PromoterAI		-0.044	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3820897; hg19: chr2-3642361;