18-322522-C-T

Position:

• chr18-322522-C-T

Variant summary

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

The ENST00000400256.5(COLEC12):​c.2064-715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,194 control chromosomes in the GnomAD database, including 3,013 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 0.18 (3013 hom., cov: 32)
• Consequence: COLEC12 ENST00000400256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLEC12	NM_130386.3	c.2064-715G>A		intron_variant		ENST00000400256.5	NP_569057.2
COLEC12	XM_011525741.3	c.2013-715G>A		intron_variant			XP_011524043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLEC12	ENST00000400256.5	c.2064-715G>A		intron_variant		1	NM_130386.3	ENSP00000383115	P1
COLEC12	ENST00000582147.1	n.3870-715G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27316 AN: 152076 Hom.: 3015 Cov.: 32

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.179 AC: 27317 AN: 152194 Hom.: 3013 Cov.: 32 AF XY: 0.179 AC XY: 13325 AN XY: 74400

Gnomad4 AFR AF: 0.0601

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.175

Alfa AF: 0.226 Hom.: 7627

Bravo AF: 0.171

Asia WGS AF: 0.264 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
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: rs621636; hg19: chr18-322522;