rs3134069

Variant names:

• chr8-118952749-A-C
• rs3134069
• NM_001324095.2:c.-324+371A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-118952749-A-C
• chr8-118952749-A-G

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+371A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 152,166 control chromosomes in the GnomAD database, including 849 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 (849 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 61 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+371A>C		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+371A>C		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: 14332 AN: 152046 Hom.: 841 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0695

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

GnomAD4 genome AF: 0.0943 AC: 14348 AN: 152166 Hom.: 849 Cov.: 32 AF XY: 0.0928 AC XY: 6905 AN XY: 74384

African (AFR) AF: 0.170 AC: 7074 AN: 41506

American (AMR) AF: 0.120 AC: 1826 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3470

East Asian (EAS) AF: 0.128 AC: 660 AN: 5146

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4820

European-Finnish (FIN) AF: 0.0382 AC: 406 AN: 10616

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

European-Non Finnish (NFE) AF: 0.0560 AC: 3811 AN: 68014

Other (OTH) AF: 0.0683 AC: 144 AN: 2108

Alfa AF: 0.0621 Hom.: 553

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	1.4
DANN	Benign	0.24
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs3134069; hg19: chr8-119964988;