rs2450083

Variant names:

• chr8-119051303-T-C
• rs2450083
• NM_001324095.2:c.-60+13153T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001324095.2(COLEC10):​c.-60+13153T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,036 control chromosomes in the GnomAD database, including 27,019 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 0.58 (27019 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 17 publications found

Genes affected

COLEC10 (HGNC:2220): (collectin subfamily member 10) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]

COLEC10 Gene-Disease associations (from GenCC):

• 3MC syndrome 3

  Inheritance: AR Classification: STRONG Submitted by: G2P
• 3MC syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-60+13153T>C		intron_variant	Intron 3 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-59-38377T>C		intron_variant	Intron 1 of 5		XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000521788.1	n.236-38377T>C		intron_variant	Intron 2 of 6	3

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88731 AN: 151918 Hom.: 26966 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.584 AC: 88838 AN: 152036 Hom.: 27019 Cov.: 32 AF XY: 0.586 AC XY: 43519 AN XY: 74262

African (AFR) AF: 0.755 AC: 31325 AN: 41470

American (AMR) AF: 0.521 AC: 7958 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2189 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3373 AN: 5180

South Asian (SAS) AF: 0.545 AC: 2628 AN: 4818

European-Finnish (FIN) AF: 0.542 AC: 5702 AN: 10524

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33901 AN: 67994

Other (OTH) AF: 0.581 AC: 1225 AN: 2110

Alfa AF: 0.523 Hom.: 33586

Bravo AF: 0.590

Asia WGS AF: 0.631 AC: 2196 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2450083; hg19: chr8-120063542;