rs16892015

Positions:

• chr8-119100829-A-C

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
COLEC10	NM_006438.5	c.293-1519A>C		intron_variant		ENST00000332843.3	NP_006429.2
COLEC10	NM_001324095.2	c.86-1519A>C		intron_variant			NP_001311024.1
COLEC10	XM_005250756.4	c.86-1519A>C		intron_variant			XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000332843.3	c.293-1519A>C		intron_variant		1	NM_006438.5	ENSP00000332723.2
COLEC10	ENST00000521788.1	n.380-1519A>C		intron_variant		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

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.0223

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.0644

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0226

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0260 Hom.: 13

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs16892015; hg19: chr8-120113068;