rs1485305

Variant names:

• chr8-118998281-A-T
• rs1485305
• NM_001324095.2:c.-323-39155A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001324095.2(COLEC10):​c.-323-39155A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,950 control chromosomes in the GnomAD database, including 23,561 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 0.54 (23561 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-323-39155A>T		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+45903A>T		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+2708A>T		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81934 AN: 151832 Hom.: 23522 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.540 AC: 82024 AN: 151950 Hom.: 23561 Cov.: 32 AF XY: 0.542 AC XY: 40285 AN XY: 74266

African (AFR) AF: 0.746 AC: 30929 AN: 41450

American (AMR) AF: 0.479 AC: 7310 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1760 AN: 3466

East Asian (EAS) AF: 0.580 AC: 2990 AN: 5152

South Asian (SAS) AF: 0.556 AC: 2678 AN: 4814

European-Finnish (FIN) AF: 0.467 AC: 4932 AN: 10556

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29903 AN: 67940

Other (OTH) AF: 0.538 AC: 1134 AN: 2106

Alfa AF: 0.500 Hom.: 2483

Bravo AF: 0.547

Asia WGS AF: 0.560 AC: 1949 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1485305; hg19: chr8-120010520;