rs644435

Positions:

• chr18-355944-A-G

Variant summary

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

The NM_130386.3(COLEC12):​c.181+1456T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,094 control chromosomes in the GnomAD database, including 14,059 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 0.40 (14059 hom., cov: 32)
• Consequence: COLEC12 NM_130386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLEC12	NM_130386.3	c.181+1456T>C		intron_variant		ENST00000400256.5
COLEC12	XM_011525741.3	c.130+1456T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLEC12	ENST00000400256.5	c.181+1456T>C		intron_variant		1	NM_130386.3	P1
COLEC12	ENST00000582147.1	n.389+1456T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60918 AN: 151976 Hom.: 14017 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.401 AC: 61013 AN: 152094 Hom.: 14059 Cov.: 32 AF XY: 0.400 AC XY: 29706 AN XY: 74320

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.347

Alfa AF: 0.317 Hom.: 13607

Bravo AF: 0.405

Asia WGS AF: 0.195 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.42

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: rs644435; hg19: chr18-355944;