rs7839059

Variant names:

• chr8-118964303-C-A
• rs7839059
• NM_001324095.2:c.-324+11925C>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.-324+11925C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,936 control chromosomes in the GnomAD database, including 12,925 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 0.40 (12925 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 28 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+11925C>A		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+11925C>A		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: 0.401 AC: 60844 AN: 151818 Hom.: 12882 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.401 AC: 60935 AN: 151936 Hom.: 12925 Cov.: 32 AF XY: 0.395 AC XY: 29339 AN XY: 74230

African (AFR) AF: 0.552 AC: 22864 AN: 41430

American (AMR) AF: 0.376 AC: 5738 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1346 AN: 5140

South Asian (SAS) AF: 0.363 AC: 1745 AN: 4808

European-Finnish (FIN) AF: 0.279 AC: 2942 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23707 AN: 67950

Other (OTH) AF: 0.413 AC: 872 AN: 2110

Alfa AF: 0.362 Hom.: 36956

Bravo AF: 0.411

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs7839059; hg19: chr8-119976542;