rs3102735

Positions:

• chr8-118952831-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001324095.2(COLEC10):​c.-324+453T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,208 control chromosomes in the GnomAD database, including 2,129 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 0.16 (2129 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+453T>C		intron_variant			NP_001311024.1
COLEC10	XM_005250756.4	c.-60+453T>C		intron_variant			XP_005250813.1
		n.118952831T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25068 AN: 152088 Hom.: 2121 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.165 AC: 25092 AN: 152208 Hom.: 2129 Cov.: 32 AF XY: 0.162 AC XY: 12086 AN XY: 74422

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.150

Alfa AF: 0.145 Hom.: 2150

Bravo AF: 0.172

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3102735; hg19: chr8-119965070;