8-118965553-G-C

Position:

• chr8-118965553-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001324095.2(COLEC10):​c.-324+13175G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,738 control chromosomes in the GnomAD database, including 33,433 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 0.65 (33433 hom., cov: 31)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+13175G>C		intron_variant			NP_001311024.1
COLEC10	XM_005250756.4	c.-60+13175G>C		intron_variant			XP_005250813.1
		n.118965553G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98532 AN: 151620 Hom.: 33377 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.650 AC: 98639 AN: 151738 Hom.: 33433 Cov.: 31 AF XY: 0.651 AC XY: 48248 AN XY: 74100

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.650

Alfa AF: 0.581 Hom.: 14551

Bravo AF: 0.656

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2062375; hg19: chr8-119977792;