NM_130386.3:c.59-57879G>A

Variant names:

• chr18-415401-C-T
• rs1940436
• NM_130386.3:c.59-57879G>A

Variant summary

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

The NM_130386.3(COLEC12):​c.59-57879G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,954 control chromosomes in the GnomAD database, including 5,527 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 0.26 (5527 hom., cov: 31)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.860
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC12	NM_130386.3	c.59-57879G>A		intron_variant	Intron 2 of 9	ENST00000400256.5	NP_569057.2
COLEC12	XM_011525741.3	c.8-57879G>A		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.59-57879G>A		intron_variant	Intron 2 of 9	1	NM_130386.3	ENSP00000383115.3
COLEC12	ENST00000582147.1	n.267-57879G>A		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38941 AN: 151838 Hom.: 5517 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.256 AC: 38975 AN: 151954 Hom.: 5527 Cov.: 31 AF XY: 0.254 AC XY: 18883 AN XY: 74246

African (AFR) AF: 0.188 AC: 7786 AN: 41468

American (AMR) AF: 0.407 AC: 6217 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 994 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2101 AN: 5134

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4816

European-Finnish (FIN) AF: 0.178 AC: 1874 AN: 10544

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.266 AC: 18062 AN: 67954

Other (OTH) AF: 0.271 AC: 570 AN: 2104

Alfa AF: 0.188 Hom.: 608

Bravo AF: 0.273

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.53
PhyloP100		0.86
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: rs1940436; hg19: chr18-415401;