12-9703362-T-G

Variant names:

• chr12-9703362-T-G
• rs11052552
• NM_001441809.1:c.253-922A>C

Variant summary

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

The NM_001441809.1(CLECL1):​c.253-922A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 150,832 control chromosomes in the GnomAD database, including 15,235 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 0.43 (15235 hom., cov: 31)
• Consequence: CLECL1 NM_001441809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 40 publications found

Genes affected

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]

ENSG00000293488 (HGNC:):

LINC02390 (HGNC:53317): (long intergenic non-protein coding RNA 2390)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001441809.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLECL1	NM_001441809.1		c.253-922A>C		intron	N/A	NP_001428738.1
	CLECL1	NM_001441810.1		c.*3-922A>C		intron	N/A	NP_001428739.1
	CLECL1	NM_001441811.1		c.223-922A>C		intron	N/A	NP_001428740.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293488	ENST00000702603.2		n.416-922A>C		intron	N/A
	ENSG00000293488	ENST00000730418.1		n.564-922A>C		intron	N/A
	ENSG00000293488	ENST00000730419.1		n.146-922A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64579 AN: 150726 Hom.: 15231 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.428 AC: 64594 AN: 150832 Hom.: 15235 Cov.: 31 AF XY: 0.426 AC XY: 31413 AN XY: 73682

African (AFR) AF: 0.213 AC: 8718 AN: 41000

American (AMR) AF: 0.507 AC: 7686 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1604 AN: 3458

East Asian (EAS) AF: 0.616 AC: 3180 AN: 5160

South Asian (SAS) AF: 0.498 AC: 2376 AN: 4772

European-Finnish (FIN) AF: 0.427 AC: 4411 AN: 10324

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35059 AN: 67650

Other (OTH) AF: 0.457 AC: 957 AN: 2094

Alfa AF: 0.489 Hom.: 41180

Bravo AF: 0.426

Asia WGS AF: 0.538 AC: 1868 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11052552; hg19: chr12-9855958;