rs1905776

Positions:

• chr8-119007413-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-323-30023C>T		intron_variant			NP_001311024.1
COLEC10	XM_005250756.4	c.-60+55035C>T		intron_variant			XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000521788.1	n.123-2028C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.236

Alfa AF: 0.195 Hom.: 1682

Bravo AF: 0.204

Asia WGS AF: 0.255 AC: 885 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1905776; hg19: chr8-120019652;