rs11662321

chr18-404000-T-G

Variant summary

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

The NM_130386.3(COLEC12):c.59-46478A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,158 control chromosomes in the GnomAD database, including 5,332 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 0.24 (5332 hom., cov: 33)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLEC12	NM_130386.3	c.59-46478A>C		intron_variant		ENST00000400256.5
COLEC12	XM_011525741.3	c.8-46478A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLEC12	ENST00000400256.5	c.59-46478A>C		intron_variant		1	NM_130386.3	P1
COLEC12	ENST00000582147.1	n.267-46478A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35907 AN: 152040 Hom.: 5322 Cov.: 33

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.236 AC: 35925 AN: 152158 Hom.: 5332 Cov.: 33 AF XY: 0.241 AC XY: 17943 AN XY: 74370

Gnomad4 AFR AF: 0.0573

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.230

Alfa AF: 0.302 Hom.: 6810

Bravo AF: 0.209

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.1
Dann	Benign	0.31

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: rs11662321; hg19: chr18-404000;