18-355944-A-G

Variant names:

• chr18-355944-A-G
• rs644435
• NM_130386.3:c.181+1456T>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.181+1456T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,094 control chromosomes in the GnomAD database, including 14,059 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 0.40 (14059 hom., cov: 32)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130386.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC12	NM_130386.3	MANE Select	c.181+1456T>C		intron	N/A	NP_569057.2	Q5KU26

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC12	ENST00000400256.5	TSL:1 MANE Select	c.181+1456T>C		intron	N/A	ENSP00000383115.3	Q5KU26
	COLEC12	ENST00000851798.1		c.130+1456T>C		intron	N/A	ENSP00000521857.1
	COLEC12	ENST00000851799.1		c.181+1456T>C		intron	N/A	ENSP00000521858.1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60918 AN: 151976 Hom.: 14017 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.401 AC: 61013 AN: 152094 Hom.: 14059 Cov.: 32 AF XY: 0.400 AC XY: 29706 AN XY: 74320

African (AFR) AF: 0.635 AC: 26341 AN: 41496

American (AMR) AF: 0.343 AC: 5245 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3468

East Asian (EAS) AF: 0.107 AC: 556 AN: 5178

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4386 AN: 10568

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21481 AN: 67982

Other (OTH) AF: 0.347 AC: 730 AN: 2104

Alfa AF: 0.334 Hom.: 37348

Bravo AF: 0.405

Asia WGS AF: 0.195 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.97
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: rs644435; hg19: chr18-355944;