18-373670-C-T

Variant names:

• chr18-373670-C-T
• rs9945820
• NM_130386.3:c.59-16148G>A

Variant summary

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

The NM_130386.3(COLEC12):​c.59-16148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,038 control chromosomes in the GnomAD database, including 3,628 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 0.21 (3628 hom., cov: 32)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

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]

LOC107985155 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC12	NM_130386.3	c.59-16148G>A		intron_variant	Intron 2 of 9	ENST00000400256.5	NP_569057.2
COLEC12	XM_011525741.3	c.8-16148G>A		intron_variant	Intron 1 of 8		XP_011524043.1
LOC107985155	XR_007066264.1	n.4280C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC12	ENST00000400256.5	c.59-16148G>A		intron_variant	Intron 2 of 9	1	NM_130386.3	ENSP00000383115.3
COLEC12	ENST00000582147.1	n.267-16148G>A		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32258 AN: 151920 Hom.: 3619 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.212 AC: 32295 AN: 152038 Hom.: 3628 Cov.: 32 AF XY: 0.211 AC XY: 15655 AN XY: 74326

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0220

Gnomad4 SAS AF: 0.0579

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.220

Alfa AF: 0.205 Hom.: 4484

Bravo AF: 0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.60

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: rs9945820; hg19: chr18-373670;