8-118965098-A-G

Variant names:

• chr8-118965098-A-G
• rs12679857
• NM_001324095.2:c.-324+12720A>G

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+12720A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,024 control chromosomes in the GnomAD database, including 10,233 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 0.36 (10233 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 16 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+12720A>G		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+12720A>G		intron_variant	Intron 1 of 5		XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54397 AN: 151906 Hom.: 10226 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.358 AC: 54428 AN: 152024 Hom.: 10233 Cov.: 32 AF XY: 0.364 AC XY: 27057 AN XY: 74312

African (AFR) AF: 0.449 AC: 18630 AN: 41454

American (AMR) AF: 0.292 AC: 4466 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2520 AN: 5144

South Asian (SAS) AF: 0.400 AC: 1933 AN: 4828

European-Finnish (FIN) AF: 0.390 AC: 4127 AN: 10584

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20331 AN: 67952

Other (OTH) AF: 0.345 AC: 728 AN: 2112

Alfa AF: 0.321 Hom.: 20453

Bravo AF: 0.352

Asia WGS AF: 0.471 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.79
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs12679857; hg19: chr8-119977337;