8-118995181-T-A

Variant names:

• chr8-118995181-T-A
• rs2062377
• NM_001324095.2:c.-323-42255T>A

Variant summary

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

The NM_001324095.2(COLEC10):​c.-323-42255T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,096 control chromosomes in the GnomAD database, including 34,898 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 0.67 (34898 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503
• Publications: 48 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC10	NM_001324095.2		c.-323-42255T>A		intron	N/A	NP_001311024.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101058 AN: 151978 Hom.: 34843 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.665 AC: 101165 AN: 152096 Hom.: 34898 Cov.: 32 AF XY: 0.668 AC XY: 49640 AN XY: 74362

African (AFR) AF: 0.858 AC: 35633 AN: 41530

American (AMR) AF: 0.601 AC: 9175 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2309 AN: 3468

East Asian (EAS) AF: 0.743 AC: 3830 AN: 5156

South Asian (SAS) AF: 0.688 AC: 3318 AN: 4822

European-Finnish (FIN) AF: 0.579 AC: 6128 AN: 10580

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38775 AN: 67968

Other (OTH) AF: 0.669 AC: 1415 AN: 2114

Alfa AF: 0.600 Hom.: 15022

Bravo AF: 0.669

Asia WGS AF: 0.744 AC: 2586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.63
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2062377; hg19: chr8-120007420;