NM_001324095.2:c.-323-41304T>C

Variant names:

• chr8-118996132-T-C
• rs6469792
• NM_001324095.2:c.-323-41304T>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.-323-41304T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,072 control chromosomes in the GnomAD database, including 29,789 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 0.61 (29789 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 14 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-323-41304T>C		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+43754T>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+559T>C		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93175 AN: 151954 Hom.: 29741 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.613 AC: 93274 AN: 152072 Hom.: 29789 Cov.: 32 AF XY: 0.615 AC XY: 45684 AN XY: 74320

African (AFR) AF: 0.800 AC: 33217 AN: 41510

American (AMR) AF: 0.539 AC: 8229 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3013 AN: 5152

South Asian (SAS) AF: 0.644 AC: 3107 AN: 4824

European-Finnish (FIN) AF: 0.526 AC: 5565 AN: 10570

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36159 AN: 67964

Other (OTH) AF: 0.622 AC: 1312 AN: 2110

Alfa AF: 0.560 Hom.: 44839

Bravo AF: 0.617

Asia WGS AF: 0.636 AC: 2213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs6469792; hg19: chr8-120008371;