8-119032590-G-A

Variant names:

• chr8-119032590-G-A
• rs6469804
• NM_001324095.2:c.-323-4846G>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.-323-4846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,056 control chromosomes in the GnomAD database, including 36,819 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 0.68 (36819 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 51 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-323-4846G>A		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-59-57090G>A		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.235+23037G>A		intron_variant	Intron 2 of 6	3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102844 AN: 151938 Hom.: 36762 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.677 AC: 102957 AN: 152056 Hom.: 36819 Cov.: 32 AF XY: 0.679 AC XY: 50488 AN XY: 74304

African (AFR) AF: 0.920 AC: 38208 AN: 41540

American (AMR) AF: 0.615 AC: 9397 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2334 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4030 AN: 5150

South Asian (SAS) AF: 0.692 AC: 3335 AN: 4816

European-Finnish (FIN) AF: 0.575 AC: 6075 AN: 10564

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37573 AN: 67930

Other (OTH) AF: 0.676 AC: 1426 AN: 2108

Alfa AF: 0.596 Hom.: 119740

Bravo AF: 0.687

Asia WGS AF: 0.762 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs6469804; hg19: chr8-120044829;