18-433431-G-A

Position:

• chr18-433431-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130386.3(COLEC12):​c.58+47276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,916 control chromosomes in the GnomAD database, including 7,325 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 0.30 (7325 hom., cov: 31)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

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]

COLEC12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLEC12	NM_130386.3	c.58+47276C>T		intron_variant		ENST00000400256.5	NP_569057.2
COLEC12	XM_011525741.3	c.7+67077C>T		intron_variant			XP_011524043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLEC12	ENST00000400256.5	c.58+47276C>T		intron_variant		1	NM_130386.3	ENSP00000383115.3
COLEC12	ENST00000582147.1	n.266+47276C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45920 AN: 151798 Hom.: 7313 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.302 AC: 45951 AN: 151916 Hom.: 7325 Cov.: 31 AF XY: 0.302 AC XY: 22391 AN XY: 74256

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.318

Alfa AF: 0.306 Hom.: 9061

Bravo AF: 0.318

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs2186830; hg19: chr18-433431;