rs3134070

Variant names:

• chr8-118952785-C-T
• rs3134070
• NM_001324095.2:c.-324+407C>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.-324+407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,200 control chromosomes in the GnomAD database, including 850 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 0.094 (850 hom., cov: 33)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 68 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+407C>T		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+407C>T		intron_variant	Intron 1 of 5		XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14346 AN: 152082 Hom.: 842 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0944 AC: 14362 AN: 152200 Hom.: 850 Cov.: 33 AF XY: 0.0929 AC XY: 6913 AN XY: 74408

African (AFR) AF: 0.171 AC: 7079 AN: 41514

American (AMR) AF: 0.120 AC: 1831 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.128 AC: 663 AN: 5172

South Asian (SAS) AF: 0.0382 AC: 184 AN: 4822

European-Finnish (FIN) AF: 0.0382 AC: 405 AN: 10596

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0560 AC: 3812 AN: 68012

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0842 Hom.: 126

Bravo AF: 0.105

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.84
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs3134070; hg19: chr8-119965024;