rs4798145

Positions:

• chr18-407958-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
COLEC12	NM_130386.3	c.59-50436A>G		intron_variant		ENST00000400256.5
COLEC12	XM_011525741.3	c.8-50436A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLEC12	ENST00000400256.5	c.59-50436A>G		intron_variant		1	NM_130386.3	P1
COLEC12	ENST00000582147.1	n.267-50436A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.482

Alfa AF: 0.522 Hom.: 27796

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

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: rs4798145; hg19: chr18-407958;