12-10098421-G-A

Variant names:

• chr12-10098421-G-A
• rs6488255
• NM_016511.4:c.115+387C>T

Variant summary

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

The NM_016511.4(CLEC1A):​c.115+387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,994 control chromosomes in the GnomAD database, including 20,313 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 0.46 (20313 hom., cov: 32)
• Consequence: CLEC1A NM_016511.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 7 publications found

Genes affected

CLEC1A (HGNC:24355): (C-type lectin domain family 1 member A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The encoded protein may play a role in regulating dendritic cell function. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016511.4. 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
	CLEC1A	NM_016511.4	MANE Select	c.115+387C>T		intron	N/A	NP_057595.2
	CLEC1A	NM_001297748.2		c.115+387C>T		intron	N/A	NP_001284677.1
	CLEC1A	NM_001297750.2		c.-248+387C>T		intron	N/A	NP_001284679.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC1A	ENST00000315330.8	TSL:1 MANE Select	c.115+387C>T		intron	N/A	ENSP00000326407.4
	CLEC1A	ENST00000457018.6	TSL:2	c.115+387C>T		intron	N/A	ENSP00000415048.2
	CLEC1A	ENST00000420265.2	TSL:2	c.115+387C>T		intron	N/A	ENSP00000417010.2

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70178 AN: 151876 Hom.: 20324 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.462 AC: 70158 AN: 151994 Hom.: 20313 Cov.: 32 AF XY: 0.460 AC XY: 34157 AN XY: 74272

African (AFR) AF: 0.128 AC: 5306 AN: 41420

American (AMR) AF: 0.444 AC: 6790 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1158 AN: 5176

South Asian (SAS) AF: 0.399 AC: 1920 AN: 4814

European-Finnish (FIN) AF: 0.633 AC: 6680 AN: 10552

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.650 AC: 44191 AN: 67974

Other (OTH) AF: 0.517 AC: 1089 AN: 2106

Alfa AF: 0.582 Hom.: 86686

Bravo AF: 0.431

Asia WGS AF: 0.292 AC: 1014 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		0.61
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: rs6488255; hg19: chr12-10251020;