Variant 12-8518219-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2

The NM_080387.5(CLEC4D):c.177G>A(p.Glu59Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,451,264 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0010 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0017 ( 6 hom. )

Consequence

CLEC4D
NM_080387.5 synonymous

Scores

Clinical Significance

Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: -0.0650

Variant links:

Genes affected

CLEC4D (HGNC:14554): (C-type lectin domain family 4 member D) 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. 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]

CLEC4D links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 12-8518219-G-A is Benign according to our data. Variant chr12-8518219-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1285021.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr12-8518219-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.065 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC4D	NM_080387.5 link	c.177G>A	p.Glu59Glu	synonymous_variant	3/6	ENST00000299665.3	NP_525126.2	Q8WXI8
CLEC4D	XM_011520632.3 link	c.177G>A	p.Glu59Glu	synonymous_variant	4/7		XP_011518934.1	Q8WXI8
CLEC4D	XM_047428771.1 link	c.177G>A	p.Glu59Glu	synonymous_variant	3/6		XP_047284727.1
CLEC4D	XM_047428772.1 link	c.177G>A	p.Glu59Glu	synonymous_variant	3/6		XP_047284728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC4D	ENST00000299665.3 link	c.177G>A	p.Glu59Glu	synonymous_variant	3/6	1	NM_080387.5	ENSP00000299665.2		Q8WXI8
CLEC4D	ENST00000382064.6 link	c.177G>A	p.Glu59Glu	synonymous_variant	4/6	3		ENSP00000371496.2		A6NHA5

Frequencies

GnomAD3 genomes

AF:

0.00104

AC:

158

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000523

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00517

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00165

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00129

AC:

320

AN:

248252

Hom.:

AF XY:

0.00144

AC XY:

194

AN XY:

134258

show subpopulations

Gnomad AFR exome

AF:

0.000378

Gnomad AMR exome

AF:

0.000874

Gnomad ASJ exome

AF:

0.000300

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00319

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00152

Gnomad OTH exome

AF:

0.00198

GnomAD4 exome

AF:

0.00173

AC:

2243

AN:

1298908

Hom.:

Cov.:

AF XY:

0.00180

AC XY:

1176

AN XY:

654326

show subpopulations

Gnomad4 AFR exome

AF:

0.000328

Gnomad4 AMR exome

AF:

0.000968

Gnomad4 ASJ exome

AF:

0.000438

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00380

Gnomad4 FIN exome

AF:

0.000319

Gnomad4 NFE exome

AF:

0.00182

Gnomad4 OTH exome

AF:

0.00151

GnomAD4 genome

AF:

0.00104

AC:

159

AN:

152356

Hom.:

Cov.:

AF XY:

0.00103

AC XY:

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.000264

Gnomad4 AMR

AF:

0.000523

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.00165

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000656

Hom.:

Bravo

AF:

0.000997

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.70

DANN

Benign

0.40

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over