8-119039999-T-C

Variant names:

• chr8-119039999-T-C
• rs6993813
• NM_001324095.2:c.-60+1849T>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+1849T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,922 control chromosomes in the GnomAD database, including 28,320 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 0.60 (28320 hom., cov: 31)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 52 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001324095.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC10	NM_001324095.2		c.-60+1849T>C		intron	N/A	NP_001311024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC10	ENST00000521788.1	TSL:3	n.235+30446T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91438 AN: 151804 Hom.: 28272 Cov.: 31

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.603 AC: 91544 AN: 151922 Hom.: 28320 Cov.: 31 AF XY: 0.604 AC XY: 44886 AN XY: 74284

African (AFR) AF: 0.745 AC: 30874 AN: 41434

American (AMR) AF: 0.549 AC: 8383 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2300 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3218 AN: 5156

South Asian (SAS) AF: 0.668 AC: 3213 AN: 4810

European-Finnish (FIN) AF: 0.533 AC: 5624 AN: 10542

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36123 AN: 67940

Other (OTH) AF: 0.620 AC: 1308 AN: 2110

Alfa AF: 0.558 Hom.: 105766

Bravo AF: 0.606

Asia WGS AF: 0.657 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.026
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6993813; hg19: chr8-120052238;