Genetic Variant CLEC11A:c.*22C>T (chr19-50725489-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.295

Publications

21 publications found

Variant links:

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]

CLEC11A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC11A	NM_002975.3 link	c.*22C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000250340.9	NP_002966.1	Q9Y240

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC11A	ENST00000250340.9 link	c.*22C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_002975.3	ENSP00000250340.3		Q9Y240
CLEC11A	ENST00000599973.1 link	c.*89C>T		downstream_gene_variant		1		ENSP00000471075.1		M0R081

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35370

AN:

152082

Hom.:

4627

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.272

AC XY:

188061

AN XY:

690466

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

16606

33212

49819

66425

83031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9772

19544

29316

39088

48860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.232

AC:

35385

AN:

152200

Hom.:

4632

Cov.:

AF XY:

0.237

AC XY:

17601

AN XY:

74404

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.256

AC:

17428

AN:

67988

Other (OTH)

AF:

0.253

AC:

535

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1385

2770

4155

5540

6925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

6.1

(source)

DANN

Benign

0.70

PhyloP100

0.29

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over