Genetic Variant CLEC17A:c.*251T>C (chr19-14610447-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001204118.2(CLEC17A):c.*251T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 510,290 control chromosomes in the GnomAD database, including 19,447 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 0.21 ( 4207 hom., cov: 31)

Exomes 𝑓: 0.27 ( 15240 hom. )

Consequence

CLEC17A
NM_001204118.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.397

Publications

9 publications found

Variant links:

Genes affected

CLEC17A (HGNC:34520): (C-type lectin domain containing 17A) Enables fucose binding activity; identical protein binding activity; and mannose binding activity. Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

CLEC17A links:

ADGRE3 (HGNC:23647): (adhesion G protein-coupled receptor E3) This gene encodes a member of the class B seven-span transmembrane (TM7) receptor family expressed predominantly by cells of the immune system. Family members are characterized by an extended extracellular region with a variable number of N-terminal epidermal growth factor (EGF)-like domains coupled to a TM7 domain via a mucin-like spacer domain. This gene is closely linked to the gene encoding egf-like molecule containing mucin-like hormone receptor 2 on chromosome 19. This protein may play a role in myeloid-myeloid interactions during immune and inflammatory responses. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2014]

ADGRE3 links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC17A	NM_001204118.2 link	c.*251T>C		3_prime_UTR_variant	Exon 14 of 14	ENST00000417570.6	NP_001191047.1	Q6ZS10-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC17A	ENST00000417570.6 link	c.*251T>C		3_prime_UTR_variant	Exon 14 of 14	1	NM_001204118.2	ENSP00000393719.2		Q6ZS10-1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31556

AN:

151830

Hom.:

4202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0494

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.421

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.206

GnomAD4 exome

AF:

0.275

AC:

98518

AN:

358342

Hom.:

15240

Cov.:

AF XY:

0.283

AC XY:

53400

AN XY:

188810

show subpopulations

African (AFR)

AF:

0.0490

AC:

514

AN:

10490

American (AMR)

AF:

0.325

AC:

4889

AN:

15030

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

2092

AN:

11126

East Asian (EAS)

AF:

0.476

AC:

11333

AN:

23784

South Asian (SAS)

AF:

0.390

AC:

15697

AN:

40262

European-Finnish (FIN)

AF:

0.342

AC:

7337

AN:

21444

Middle Eastern (MID)

AF:

0.265

AC:

428

AN:

1616

European-Non Finnish (NFE)

AF:

0.239

AC:

51108

AN:

213840

Other (OTH)

AF:

0.247

AC:

5120

AN:

20750

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

3169

6338

9506

12675

15844

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.208

AC:

31565

AN:

151948

Hom.:

4207

Cov.:

AF XY:

0.217

AC XY:

16139

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.0494

AC:

2052

AN:

41498

American (AMR)

AF:

0.296

AC:

4505

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

676

AN:

3470

East Asian (EAS)

AF:

0.421

AC:

2170

AN:

5154

South Asian (SAS)

AF:

0.380

AC:

1830

AN:

4820

European-Finnish (FIN)

AF:

0.337

AC:

3552

AN:

10534

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.237

AC:

16072

AN:

67926

Other (OTH)

AF:

0.208

AC:

439

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1181

2361

3542

4722

5903

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.230

Hom.:

7137

Bravo

AF:

0.193

Asia WGS

AF:

0.394

AC:

1370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.2

(source)

DANN

Benign

0.86

PhyloP100

0.40

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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19-14610447-T-C

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