rs11662321

Variant names:

• chr18-404000-T-G
• rs11662321
• NM_130386.3:c.59-46478A>C

Variant summary

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

The NM_130386.3(COLEC12):​c.59-46478A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,158 control chromosomes in the GnomAD database, including 5,332 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 0.24 (5332 hom., cov: 33)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 4 publications found

Genes affected

COLEC12 (HGNC:16016): (collectin subfamily member 12) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. This protein is a scavenger receptor that displays several functions associated with host defense. It can bind to carbohydrate antigens on microorganisms, facilitating their recognition and removal. It also mediates the recognition, internalization, and degradation of oxidatively modified low density lipoprotein by vascular endothelial cells. [provided by RefSeq, May 2018]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC12	NM_130386.3	c.59-46478A>C		intron_variant	Intron 2 of 9	ENST00000400256.5	NP_569057.2
COLEC12	XM_011525741.3	c.8-46478A>C		intron_variant	Intron 1 of 8		XP_011524043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC12	ENST00000400256.5	c.59-46478A>C		intron_variant	Intron 2 of 9	1	NM_130386.3	ENSP00000383115.3
COLEC12	ENST00000582147.1	n.267-46478A>C		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35907 AN: 152040 Hom.: 5322 Cov.: 33

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.236 AC: 35925 AN: 152158 Hom.: 5332 Cov.: 33 AF XY: 0.241 AC XY: 17943 AN XY: 74370

African (AFR) AF: 0.0573 AC: 2380 AN: 41554

American (AMR) AF: 0.199 AC: 3044 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1014 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1175 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2248 AN: 4822

European-Finnish (FIN) AF: 0.349 AC: 3689 AN: 10566

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21543 AN: 67974

Other (OTH) AF: 0.230 AC: 485 AN: 2110

Alfa AF: 0.297 Hom.: 8091

Bravo AF: 0.209

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.1
DANN	Benign	0.31
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11662321; hg19: chr18-404000;