8-118965553-G-C

Variant names:

• chr8-118965553-G-C
• rs2062375
• NM_001324095.2:c.-324+13175G>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.-324+13175G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,738 control chromosomes in the GnomAD database, including 33,433 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 0.65 (33433 hom., cov: 31)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 32 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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.-324+13175G>C		intron	N/A	NP_001311024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98532 AN: 151620 Hom.: 33377 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.650 AC: 98639 AN: 151738 Hom.: 33433 Cov.: 31 AF XY: 0.651 AC XY: 48248 AN XY: 74100

African (AFR) AF: 0.851 AC: 35240 AN: 41400

American (AMR) AF: 0.591 AC: 9009 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2281 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3814 AN: 5088

South Asian (SAS) AF: 0.666 AC: 3203 AN: 4812

European-Finnish (FIN) AF: 0.556 AC: 5821 AN: 10472

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37305 AN: 67932

Other (OTH) AF: 0.650 AC: 1374 AN: 2114

Alfa AF: 0.581 Hom.: 14551

Bravo AF: 0.656

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2062375; hg19: chr8-119977792;