rs1905785

Variant names:

• chr8-119002313-T-C
• rs1905785
• NM_001324095.2:c.-323-35123T>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.-323-35123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,954 control chromosomes in the GnomAD database, including 4,302 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 0.23 (4302 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-323-35123T>C		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+49935T>C		intron_variant	Intron 1 of 5		XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000521788.1	n.122+6740T>C		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35319 AN: 151836 Hom.: 4304 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.232 AC: 35315 AN: 151954 Hom.: 4302 Cov.: 32 AF XY: 0.238 AC XY: 17699 AN XY: 74266

African (AFR) AF: 0.253 AC: 10491 AN: 41452

American (AMR) AF: 0.178 AC: 2715 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1899 AN: 5166

South Asian (SAS) AF: 0.284 AC: 1370 AN: 4820

European-Finnish (FIN) AF: 0.302 AC: 3185 AN: 10546

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14040 AN: 67936

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.225 Hom.: 640

Bravo AF: 0.224

Asia WGS AF: 0.279 AC: 966 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1905785; hg19: chr8-120014552;