rs10466829

Variant names:

• chr12-9723495-G-A
• rs10466829
• ENST00000327839.5:n.420-682C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001441804.1(CLECL1):​c.83-682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,802 control chromosomes in the GnomAD database, including 23,409 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 0.55 (23409 hom., cov: 30)
• Consequence: CLECL1 NM_001441804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 72 publications found

Genes affected

ENSG00000293488 (HGNC:):

CLECL1 (HGNC:24462): (C-type lectin like 1, pseudogene) This gene encodes a type II transmembrane, C-type lectin-like protein that is highly expressed on dendritic and B cells. This protein may act as a T-cell costimulatory molecule that enhances interleukin-4 production, and maybe involved in the regulation of the immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001441804.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLECL1	NM_001441804.1		c.83-682C>T		intron	N/A	NP_001428733.1
	CLECL1	NM_001441805.1		c.149-682C>T		intron	N/A	NP_001428734.1
	CLECL1	NM_001441806.1		c.149-682C>T		intron	N/A	NP_001428735.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293488	ENST00000327839.5	TSL:1	n.420-682C>T		intron	N/A
	ENSG00000293488	ENST00000542530.5	TSL:4	n.172-682C>T		intron	N/A
	CLECL1P	ENST00000621400.5	TSL:5	n.263-682C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83288 AN: 151682 Hom.: 23381 Cov.: 30

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.549 AC: 83360 AN: 151802 Hom.: 23409 Cov.: 30 AF XY: 0.551 AC XY: 40830 AN XY: 74162

African (AFR) AF: 0.660 AC: 27303 AN: 41340

American (AMR) AF: 0.495 AC: 7539 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2109 AN: 3472

East Asian (EAS) AF: 0.391 AC: 2021 AN: 5172

South Asian (SAS) AF: 0.566 AC: 2732 AN: 4824

European-Finnish (FIN) AF: 0.575 AC: 6033 AN: 10500

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33921 AN: 67940

Other (OTH) AF: 0.529 AC: 1116 AN: 2110

Alfa AF: 0.514 Hom.: 69512

Bravo AF: 0.541

Asia WGS AF: 0.480 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.47
PhyloP100		-2.0
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10466829;

hg19: chr12-9876091;