rs4424296

Variant names:

• chr8-119001037-C-T
• rs4424296
• NM_001324095.2:c.-323-36399C>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.-323-36399C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,990 control chromosomes in the GnomAD database, including 29,163 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 0.61 (29163 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 18 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-323-36399C>T		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+48659C>T		intron_variant	Intron 1 of 5		XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000521788.1	n.122+5464C>T		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92000 AN: 151872 Hom.: 29123 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.606 AC: 92089 AN: 151990 Hom.: 29163 Cov.: 32 AF XY: 0.608 AC XY: 45195 AN XY: 74286

African (AFR) AF: 0.798 AC: 33094 AN: 41466

American (AMR) AF: 0.545 AC: 8321 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3192 AN: 5154

South Asian (SAS) AF: 0.649 AC: 3124 AN: 4812

European-Finnish (FIN) AF: 0.527 AC: 5565 AN: 10560

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34841 AN: 67952

Other (OTH) AF: 0.613 AC: 1287 AN: 2098

Alfa AF: 0.576 Hom.: 7976

Bravo AF: 0.611

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs4424296; hg19: chr8-120013276;