rs2465403

Variant names:

• chr8-119078588-G-A
• rs2465403
• NM_006438.5:c.149-11092G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.88).
• 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 rank	MANE	Protein	UniProt
COLEC10	NM_006438.5	c.149-11092G>A		intron_variant	Intron 1 of 5	ENST00000332843.3	NP_006429.2
COLEC10	NM_001324095.2	c.-59-11092G>A		intron_variant	Intron 3 of 7		NP_001311024.1
COLEC10	XM_005250756.4	c.-59-11092G>A		intron_variant	Intron 1 of 5		XP_005250813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC10	ENST00000332843.3	c.149-11092G>A		intron_variant	Intron 1 of 5	1	NM_006438.5	ENSP00000332723.2
COLEC10	ENST00000521788.1	n.236-11092G>A		intron_variant	Intron 2 of 6	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

African (AFR) AF: 0.685 AC: 28410 AN: 41496

American (AMR) AF: 0.544 AC: 8317 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2522 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2509 AN: 5154

South Asian (SAS) AF: 0.500 AC: 2406 AN: 4816

European-Finnish (FIN) AF: 0.558 AC: 5881 AN: 10532

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41999 AN: 67970

Other (OTH) AF: 0.651 AC: 1372 AN: 2106

Alfa AF: 0.612 Hom.: 51387

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
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2465403; hg19: chr8-120090827;