8-119007413-C-T

Variant names:

• chr8-119007413-C-T
• rs1905776
• NM_001324095.2:c.-323-30023C>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.-323-30023C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 145,568 control chromosomes in the GnomAD database, including 3,492 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 0.20 (3492 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001324095.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC10	NM_001324095.2		c.-323-30023C>T		intron	N/A	NP_001311024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLEC10	ENST00000521788.1	TSL:3	n.123-2028C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 29484 AN: 145456 Hom.: 3476 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.203 AC: 29518 AN: 145568 Hom.: 3492 Cov.: 32 AF XY: 0.203 AC XY: 14456 AN XY: 71328

African (AFR) AF: 0.211 AC: 7456 AN: 35398

American (AMR) AF: 0.254 AC: 3814 AN: 14996

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 754 AN: 3464

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5150

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4826

European-Finnish (FIN) AF: 0.139 AC: 1471 AN: 10568

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12935 AN: 67916

Other (OTH) AF: 0.236 AC: 482 AN: 2046

Alfa AF: 0.195 Hom.: 2288

Bravo AF: 0.204

Asia WGS AF: 0.255 AC: 885 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.77
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs1905776; hg19: chr8-120019652;