NM_001324095.2:c.-324+1292A>C

Variant names:

• chr8-118953670-A-C
• rs1564861
• NM_001324095.2:c.-324+1292A>C

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+1292A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,006 control chromosomes in the GnomAD database, including 14,243 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 0.43 (14243 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+1292A>C		intron_variant	Intron 1 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-60+1292A>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: 0.427 AC: 64878 AN: 151888 Hom.: 14215 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.427 AC: 64941 AN: 152006 Hom.: 14243 Cov.: 32 AF XY: 0.431 AC XY: 32009 AN XY: 74284

African (AFR) AF: 0.513 AC: 21273 AN: 41438

American (AMR) AF: 0.362 AC: 5535 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1638 AN: 3464

East Asian (EAS) AF: 0.455 AC: 2347 AN: 5162

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4818

European-Finnish (FIN) AF: 0.418 AC: 4410 AN: 10556

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25927 AN: 67974

Other (OTH) AF: 0.443 AC: 934 AN: 2110

Alfa AF: 0.415 Hom.: 2423

Bravo AF: 0.425

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.41
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1564861; hg19: chr8-119965909;