dbSNP rs10840759: ENSG00000284393:n.113+357C>T (chr12-8138610-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 ENST00000402465.8(ENSG00000284393):n.113+357C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 166,094 control chromosomes in the GnomAD database, including 6,935 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 0.28 ( 6365 hom., cov: 29)

Exomes 𝑓: 0.24 ( 570 hom. )

Consequence

ENSG00000284393
ENST00000402465.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.594

Publications

5 publications found

Variant links:

Genes affected

ENSG00000284393 (HGNC:):

ENSG00000284393 links:

CLEC4A (HGNC:13257): (C-type lectin domain family 4 member A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may play a role in inflammatory and immune response. Multiple transcript variants encoding distinct isoforms have been identified for this gene. 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]

CLEC4A 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC4A	NM_016184.4 link	c.*323C>T		downstream_gene_variant		ENST00000229332.12	NP_057268.1	Q9UMR7-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000284393	ENST00000402465.8 link	n.113+357C>T	intron_variant	Intron 1 of 4	2		ENSP00000384896.4	B5MCH6
CLEC4A	ENST00000229332.12 link	c.*323C>T	downstream_gene_variant		1	NM_016184.4	ENSP00000229332.5	Q9UMR7-1
CLEC4A	ENST00000345999.9 link	c.*323C>T	downstream_gene_variant		5		ENSP00000344646.3	Q9UMR7-4
ENSG00000284697	ENST00000546339.2 link	n.*62C>T	downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42041

AN:

149254

Hom.:

6346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.503

Gnomad SAS

AF:

0.312

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.284

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.282

GnomAD4 exome

AF:

0.238

AC:

3999

AN:

16804

Hom.:

570

Cov.:

AF XY:

0.236

AC XY:

2034

AN XY:

8602

show subpopulations

African (AFR)

AF:

0.303

AC:

118

AN:

390

American (AMR)

AF:

0.410

AC:

347

AN:

846

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

106

AN:

496

East Asian (EAS)

AF:

0.450

AC:

353

AN:

784

South Asian (SAS)

AF:

0.273

AC:

333

AN:

1218

European-Finnish (FIN)

AF:

0.223

AC:

154

AN:

690

Middle Eastern (MID)

AF:

0.269

AC:

AN:

European-Non Finnish (NFE)

AF:

0.206

AC:

2298

AN:

11174

Other (OTH)

AF:

0.238

AC:

269

AN:

1128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

154

308

461

615

769

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<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:

0.282

AC:

42079

AN:

149290

Hom.:

6365

Cov.:

AF XY:

0.287

AC XY:

20859

AN XY:

72792

show subpopulations

African (AFR)

AF:

0.332

AC:

13520

AN:

40700

American (AMR)

AF:

0.389

AC:

5830

AN:

14980

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

748

AN:

3464

East Asian (EAS)

AF:

0.503

AC:

2566

AN:

5106

South Asian (SAS)

AF:

0.312

AC:

1482

AN:

4746

European-Finnish (FIN)

AF:

0.258

AC:

2466

AN:

9560

Middle Eastern (MID)

AF:

0.282

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.217

AC:

14660

AN:

67488

Other (OTH)

AF:

0.285

AC:

588

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1469

2938

4408

5877

7346

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<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:

0.243

Hom.:

8978

Bravo

AF:

0.298

Asia WGS

AF:

0.392

AC:

1364

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

(source)

DANN

Benign

0.57

PhyloP100

-0.59

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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