18-398147-T-C

Variant names:

• chr18-398147-T-C
• rs3932728
• NM_130386.3:c.59-40625A>G

Variant summary

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

The NM_130386.3(COLEC12):​c.59-40625A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,136 control chromosomes in the GnomAD database, including 33,322 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 0.65 (33322 hom., cov: 33)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• 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]

LOC107985155 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC12	NM_130386.3	c.59-40625A>G		intron_variant	Intron 2 of 9	ENST00000400256.5	NP_569057.2
COLEC12	XM_011525741.3	c.8-40625A>G		intron_variant	Intron 1 of 8		XP_011524043.1
LOC107985155	XR_001753316.3	n.286-1937T>C		intron_variant	Intron 3 of 3
LOC107985155	XR_007066264.1	n.17608-1937T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC12	ENST00000400256.5	c.59-40625A>G		intron_variant	Intron 2 of 9	1	NM_130386.3	ENSP00000383115.3
COLEC12	ENST00000582147.1	n.267-40625A>G		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99055 AN: 152018 Hom.: 33321 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.651 AC: 99100 AN: 152136 Hom.: 33322 Cov.: 33 AF XY: 0.653 AC XY: 48554 AN XY: 74388

African (AFR) AF: 0.474 AC: 19662 AN: 41482

American (AMR) AF: 0.620 AC: 9489 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4277 AN: 5178

South Asian (SAS) AF: 0.864 AC: 4174 AN: 4832

European-Finnish (FIN) AF: 0.660 AC: 6974 AN: 10562

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49838 AN: 67996

Other (OTH) AF: 0.654 AC: 1384 AN: 2116

Alfa AF: 0.702 Hom.: 104399

Bravo AF: 0.634

Asia WGS AF: 0.810 AC: 2816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.034
DANN	Benign	0.36
PhyloP100		-3.3
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: rs3932728; hg19: chr18-398147; COSMIC: COSV68374249;