rs13866

Variant names:

• chr19-50725489-C-T
• rs13866
• NM_002975.3:c.*22C>T

Variant summary

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

The NM_002975.3(CLEC11A):​c.*22C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,554,738 control chromosomes in the GnomAD database, including 56,809 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 0.23 (4632 hom., cov: 33)
  • Exomes 𝑓: 0.27 (52177 hom.)
• Consequence: CLEC11A NM_002975.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 21 publications found

Genes affected

CLEC11A (HGNC:10576): (C-type lectin domain containing 11A) This gene encodes a member of the C-type lectin superfamily. The encoded protein is a secreted sulfated glycoprotein and functions as a growth factor for primitive hematopoietic progenitor cells. An alternative splice variant has been described but its biological nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002975.3. 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
	CLEC11A	NM_002975.3	MANE Select	c.*22C>T		3_prime_UTR	Exon 4 of 4	NP_002966.1	Q9Y240

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC11A	ENST00000250340.9	TSL:1 MANE Select	c.*22C>T		3_prime_UTR	Exon 4 of 4	ENSP00000250340.3	Q9Y240
	CLEC11A	ENST00000883282.1		c.*22C>T		3_prime_UTR	Exon 4 of 4	ENSP00000553341.1
	CLEC11A	ENST00000883280.1		c.*22C>T		3_prime_UTR	Exon 4 of 4	ENSP00000553339.1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35370 AN: 152082 Hom.: 4627 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.251

GnomAD2 exomes AF: 0.296 AC: 54547 AN: 184074 AF XY: 0.299

Gnomad AFR exome AF: 0.120

Gnomad AMR exome AF: 0.366

Gnomad ASJ exome AF: 0.278

Gnomad EAS exome AF: 0.346

Gnomad FIN exome AF: 0.281

Gnomad NFE exome AF: 0.265

Gnomad OTH exome AF: 0.287

GnomAD4 exome AF: 0.269 AC: 376860 AN: 1402538 Hom.: 52177 Cov.: 54 AF XY: 0.272 AC XY: 188061 AN XY: 690466

African (AFR) AF: 0.117 AC: 3731 AN: 31972

American (AMR) AF: 0.350 AC: 13249 AN: 37902

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 6375 AN: 23624

East Asian (EAS) AF: 0.356 AC: 13464 AN: 37834

South Asian (SAS) AF: 0.383 AC: 30353 AN: 79202

European-Finnish (FIN) AF: 0.265 AC: 13082 AN: 49366

Middle Eastern (MID) AF: 0.243 AC: 1353 AN: 5578

European-Non Finnish (NFE) AF: 0.259 AC: 279587 AN: 1079332

Other (OTH) AF: 0.271 AC: 15666 AN: 57728

GnomAD4 genome AF: 0.232 AC: 35385 AN: 152200 Hom.: 4632 Cov.: 33 AF XY: 0.237 AC XY: 17601 AN XY: 74404

African (AFR) AF: 0.124 AC: 5155 AN: 41568

American (AMR) AF: 0.294 AC: 4498 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1780 AN: 5154

South Asian (SAS) AF: 0.385 AC: 1857 AN: 4826

European-Finnish (FIN) AF: 0.268 AC: 2841 AN: 10584

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17428 AN: 67988

Other (OTH) AF: 0.253 AC: 535 AN: 2114

Alfa AF: 0.259 Hom.: 1878

Bravo AF: 0.229

Asia WGS AF: 0.357 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.1
DANN	Benign	0.70
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism

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: rs13866; hg19: chr19-51228746; COSMIC: COSV51574457; COSMIC: COSV51574457;