Variant rs7252229 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021155.4(CD209):c.106+11C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,613,510 control chromosomes in the GnomAD database, including 20,192 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 ( 4428 hom., cov: 33)

Exomes 𝑓: 0.14 ( 15764 hom. )

Consequence

CD209
NM_021155.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.936

Variant links:

Genes affected

CD209 (HGNC:1641): (CD209 molecule) This gene encodes a C-type lectin that functions in cell adhesion and pathogen recognition. This receptor recognizes a wide range of evolutionarily divergent pathogens with a large impact on public health, including leprosy and tuberculosis mycobacteria, the Ebola, hepatitis C, HIV-1 and Dengue viruses, and the SARS-CoV acute respiratory syndrome coronavirus. The protein is organized into four distinct domains: a C-terminal carbohydrate recognition domain, a flexible tandem-repeat neck domain, a transmembrane region and an N-terminal cytoplasmic domain involved in internalization. This gene is closely related in terms of both sequence and function to a neighboring gene, CLEC4M (Gene ID: 10332), also known as L-SIGN. The two genes differ in viral recognition and expression patterns, with this gene showing high expression on the surface of dendritic cells. Polymorphisms in the neck region are associated with protection from HIV-1 infection, while single nucleotide polymorphisms in the promoter of this gene are associated with differing resistance and susceptibility to and severity of infectious disease, including rs4804803, which is associated with SARS severity. [provided by RefSeq, May 2020]

CD209 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD209	NM_021155.4 link	c.106+11C>G		intron_variant		ENST00000315599.12	NP_066978.1	Q9NNX6-1B2R907

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD209	ENST00000315599.12 link	c.106+11C>G		intron_variant		1	NM_021155.4	ENSP00000315477.6		Q9NNX6-1

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31833

AN:

152042

Hom.:

4431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.403

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.0675

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.183

GnomAD3 exomes

AF:

0.141

AC:

35475

AN:

251434

Hom.:

3252

AF XY:

0.137

AC XY:

18638

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.407

Gnomad AMR exome

AF:

0.0917

Gnomad ASJ exome

AF:

0.141

Gnomad EAS exome

AF:

0.0717

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.141

Gnomad NFE exome

AF:

0.137

Gnomad OTH exome

AF:

0.147

GnomAD4 exome

AF:

0.138

AC:

202099

AN:

1461350

Hom.:

15764

Cov.:

AF XY:

0.137

AC XY:

99385

AN XY:

727012

show subpopulations

Gnomad4 AFR exome

AF:

0.415

Gnomad4 AMR exome

AF:

0.0980

Gnomad4 ASJ exome

AF:

0.145

Gnomad4 EAS exome

AF:

0.0561

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.141

Gnomad4 NFE exome

AF:

0.135

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

AF:

0.209

AC:

31840

AN:

152160

Hom.:

4428

Cov.:

AF XY:

0.207

AC XY:

15406

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.402

Gnomad4 AMR

AF:

0.137

Gnomad4 ASJ

AF:

0.155

Gnomad4 EAS

AF:

0.0675

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.143

Gnomad4 NFE

AF:

0.138

Gnomad4 OTH

AF:

0.182

Alfa

AF:

0.171

Hom.:

483

Bravo

AF:

0.217

Asia WGS

AF:

0.110

AC:

385

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.52

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over