rs16910526

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_197947.3(CLEC7A):c.714T>G(p.Tyr238*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0731 in 1,608,786 control chromosomes in the GnomAD database, including 4,901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.055 ( 309 hom., cov: 32)

Exomes 𝑓: 0.075 ( 4592 hom. )

Consequence

CLEC7A
NM_197947.3 stop_gained

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts P:1B:5O:1

Conservation

PhyloP100: -0.0690

Publications

174 publications found

Variant links:

Genes affected

CLEC7A (HGNC:14558): (C-type lectin domain containing 7A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. The encoded glycoprotein is a small type II membrane receptor with an extracellular C-type lectin-like domain fold and a cytoplasmic domain with an immunoreceptor tyrosine-based activation motif. It functions as a pattern-recognition receptor that recognizes a variety of beta-1,3-linked and beta-1,6-linked glucans from fungi and plants, and in this way plays a role in innate immune response. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]

CLEC7A Gene-Disease associations (from GenCC):

chronic mucocutaneous candidiasis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CLEC7A links:

ENSG00000299754 (HGNC:):

ENSG00000299754 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 12-10118488-A-C is Benign according to our data. Variant chr12-10118488-A-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 4466.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_197947.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CLEC7A	NM_197947.3	MANE Select	c.714T>G	p.Tyr238*	stop_gained	Exon 6 of 6	NP_922938.1	Q9BXN2-1
CLEC7A	NM_022570.5		c.576T>G	p.Tyr192*	stop_gained	Exon 5 of 5	NP_072092.2
CLEC7A	NM_197950.3		c.477T>G	p.Tyr159*	stop_gained	Exon 4 of 4	NP_922941.1	Q9BXN2-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CLEC7A	ENST00000304084.13	TSL:1 MANE Select	c.714T>G	p.Tyr238*	stop_gained	Exon 6 of 6	ENSP00000302569.8	Q9BXN2-1
CLEC7A	ENST00000353231.9	TSL:1	c.576T>G	p.Tyr192*	stop_gained	Exon 5 of 5	ENSP00000266456.6	Q9BXN2-2
CLEC7A	ENST00000396484.6	TSL:1	c.477T>G	p.Tyr159*	stop_gained	Exon 4 of 4	ENSP00000379743.2	Q9BXN2-5

Frequencies

GnomAD3 genomes

AF:

0.0549

AC:

8354

AN:

152146

Hom.:

310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0207

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.0468

Gnomad ASJ

AF:

0.0784

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0881

Gnomad FIN

AF:

0.0524

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0771

Gnomad OTH

AF:

0.0489

GnomAD2 exomes

AF:

0.0620

AC:

15565

AN:

251140

AF XY:

0.0652

show subpopulations

Gnomad AFR exome

AF:

0.0233

Gnomad AMR exome

AF:

0.0357

Gnomad ASJ exome

AF:

0.0810

Gnomad EAS exome

AF:

0.000218

Gnomad FIN exome

AF:

0.0542

Gnomad NFE exome

AF:

0.0764

Gnomad OTH exome

AF:

0.0692

GnomAD4 exome

AF:

0.0751

AC:

109324

AN:

1456522

Hom.:

4592

Cov.:

AF XY:

0.0761

AC XY:

55160

AN XY:

724786

show subpopulations

African (AFR)

AF:

0.0201

AC:

670

AN:

33394

American (AMR)

AF:

0.0367

AC:

1640

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.0813

AC:

2120

AN:

26086

East Asian (EAS)

AF:

0.000227

AC:

AN:

39658

South Asian (SAS)

AF:

0.0945

AC:

8141

AN:

86106

European-Finnish (FIN)

AF:

0.0571

AC:

3050

AN:

53406

Middle Eastern (MID)

AF:

0.0617

AC:

355

AN:

5752

European-Non Finnish (NFE)

AF:

0.0804

AC:

89041

AN:

1107252

Other (OTH)

AF:

0.0714

AC:

4298

AN:

60198

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.446

Heterozygous variant carriers

4560

9120

13680

18240

22800

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3250

6500

9750

13000

16250

<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:

0.0549

AC:

8357

AN:

152264

Hom.:

309

Cov.:

AF XY:

0.0538

AC XY:

4003

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0208

AC:

866

AN:

41562

American (AMR)

AF:

0.0467

AC:

715

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0784

AC:

272

AN:

3470

East Asian (EAS)

AF:

0.00174

AC:

AN:

5186

South Asian (SAS)

AF:

0.0878

AC:

423

AN:

4818

European-Finnish (FIN)

AF:

0.0524

AC:

556

AN:

10602

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0771

AC:

5243

AN:

68012

Other (OTH)

AF:

0.0479

AC:

101

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

415

830

1244

1659

2074

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0681

Hom.:

1231

Bravo

AF:

0.0530

TwinsUK

AF:

0.0887

AC:

329

ALSPAC

AF:

0.0745

AC:

287

ESP6500AA

AF:

0.0263

AC:

116

ESP6500EA

AF:

0.0790

AC:

679

ExAC

AF:

0.0631

AC:

7657

Asia WGS

AF:

0.0360

AC:

126

AN:

3478

EpiCase

AF:

0.0784

EpiControl

AF:

0.0773

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Familial chronic mucocutaneous candidiasis (2)

CLEC7A-related disorder (1)

Familial chronic mucocutaneous candidiasis;C3279774:Aspergillosis, susceptibility to (1)

not provided (1)

not specified (1)

Aspergillosis, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.011

BayesDel_noAF

Pathogenic

0.29

CADD

Pathogenic

(source)

DANN

Uncertain

0.98

Eigen

Benign

-0.082

Eigen_PC

Benign

-0.39

FATHMM_MKL

Benign

0.20

PhyloP100

-0.069

Vest4

0.34

GERP RS

-2.3

Mutation Taster

=181/19

polymorphism (auto)

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over