rs2465403

Positions:

• chr8-119078588-G-A
• chr8-119078588-G-C
• chr8-119078588-G-T

Variant summary

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

The NM_006438.5(COLEC10):​c.149-11092G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,028 control chromosomes in the GnomAD database, including 29,576 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 0.62 (29576 hom., cov: 32)
• Consequence: COLEC10 NM_006438.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLEC10	NM_006438.5	c.149-11092G>A		intron_variant		ENST00000332843.3	NP_006429.2
COLEC10	NM_001324095.2	c.-59-11092G>A		intron_variant			NP_001311024.1
COLEC10	XM_005250756.4	c.-59-11092G>A		intron_variant			XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000332843.3	c.149-11092G>A		intron_variant		1	NM_006438.5	ENSP00000332723	P1
COLEC10	ENST00000521788.1	n.236-11092G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94035 AN: 151910 Hom.: 29551 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.619 AC: 94107 AN: 152028 Hom.: 29576 Cov.: 32 AF XY: 0.614 AC XY: 45589 AN XY: 74296

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.651

Alfa AF: 0.601 Hom.: 11169

Bravo AF: 0.621

Asia WGS AF: 0.536 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2465403; hg19: chr8-120090827;