8-119000461-C-G

Position:

• chr8-119000461-C-G

Variant summary

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

The NM_001324095.2(COLEC10):​c.-323-36975C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,908 control chromosomes in the GnomAD database, including 33,325 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 (33325 hom., cov: 31)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

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]

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 = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLEC10	NM_001324095.2	c.-323-36975C>G		intron_variant
COLEC10	XM_005250756.4	c.-60+48083C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLEC10	ENST00000521788.1	n.122+4888C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98090 AN: 151790 Hom.: 33269 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.646 AC: 98197 AN: 151908 Hom.: 33325 Cov.: 31 AF XY: 0.646 AC XY: 47973 AN XY: 74210

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.646

Alfa AF: 0.577 Hom.: 14257

Bravo AF: 0.652

Asia WGS AF: 0.669 AC: 2328 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	0.79
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11995824; hg19: chr8-120012700;