rs13866

Positions:

• chr19-50725489-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC11A	NM_002975.3	c.*22C>T		3_prime_UTR_variant	4/4	ENST00000250340.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC11A	ENST00000250340.9	c.*22C>T		3_prime_UTR_variant	4/4	1	NM_002975.3	P1
CLEC11A	ENST00000599973.1			downstream_gene_variant		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

GnomAD3 exomes AF: 0.296 AC: 54547 AN: 184074 Hom.: 8221 AF XY: 0.299 AC XY: 29964 AN XY: 100126

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 SAS exome AF: 0.400

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

Gnomad4 AFR exome AF: 0.117

Gnomad4 AMR exome AF: 0.350

Gnomad4 ASJ exome AF: 0.270

Gnomad4 EAS exome AF: 0.356

Gnomad4 SAS exome AF: 0.383

Gnomad4 FIN exome AF: 0.265

Gnomad4 NFE exome AF: 0.259

Gnomad4 OTH exome AF: 0.271

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.253

Alfa AF: 0.263 Hom.: 1531

Bravo AF: 0.229

Asia WGS AF: 0.357 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.1
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

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