rs16892015

Variant names:

• chr8-119100829-A-C
• rs16892015
• NM_006438.5:c.293-1519A>C

Variant summary

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

The NM_006438.5(COLEC10):​c.293-1519A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0322 in 152,164 control chromosomes in the GnomAD database, including 120 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 0.032 (120 hom., cov: 32)
• Consequence: COLEC10 NM_006438.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_006438.5	c.293-1519A>C		intron_variant	Intron 3 of 5	ENST00000332843.3	NP_006429.2
COLEC10	NM_001324095.2	c.86-1519A>C		intron_variant	Intron 5 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.86-1519A>C		intron_variant	Intron 3 of 5		XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000332843.3	c.293-1519A>C		intron_variant	Intron 3 of 5	1	NM_006438.5	ENSP00000332723.2
COLEC10	ENST00000521788.1	n.380-1519A>C		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.0322 AC: 4892 AN: 152044 Hom.: 120 Cov.: 32

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0224

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0322 AC: 4904 AN: 152164 Hom.: 120 Cov.: 32 AF XY: 0.0349 AC XY: 2596 AN XY: 74376

African (AFR) AF: 0.0441 AC: 1832 AN: 41538

American (AMR) AF: 0.0223 AC: 341 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.0644 AC: 333 AN: 5170

South Asian (SAS) AF: 0.109 AC: 524 AN: 4814

European-Finnish (FIN) AF: 0.0226 AC: 239 AN: 10596

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0191 AC: 1299 AN: 67988

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0264 Hom.: 15

Bravo AF: 0.0317

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.25
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs16892015; hg19: chr8-120113068;