NM_130386.3:c.59-50436A>G

Variant names:

• chr18-407958-T-C
• rs4798145
• NM_130386.3:c.59-50436A>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.59-50436A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,100 control chromosomes in the GnomAD database, including 18,166 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 0.48 (18166 hom., cov: 33)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC12	NM_130386.3	c.59-50436A>G		intron_variant	Intron 2 of 9	ENST00000400256.5	NP_569057.2
COLEC12	XM_011525741.3	c.8-50436A>G		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.59-50436A>G		intron_variant	Intron 2 of 9	1	NM_130386.3	ENSP00000383115.3
COLEC12	ENST00000582147.1	n.267-50436A>G		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73510 AN: 151982 Hom.: 18159 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.484 AC: 73557 AN: 152100 Hom.: 18166 Cov.: 33 AF XY: 0.484 AC XY: 35975 AN XY: 74318

African (AFR) AF: 0.404 AC: 16764 AN: 41510

American (AMR) AF: 0.446 AC: 6822 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1666 AN: 5168

South Asian (SAS) AF: 0.698 AC: 3368 AN: 4826

European-Finnish (FIN) AF: 0.516 AC: 5443 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36170 AN: 67972

Other (OTH) AF: 0.482 AC: 1019 AN: 2112

Alfa AF: 0.516 Hom.: 34387

Bravo AF: 0.467

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.69
PhyloP100		0.25
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: rs4798145; hg19: chr18-407958;