Variant rs4804800 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.*2797C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 391,618 control chromosomes in the GnomAD database, including 139,204 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 0.81 ( 50648 hom., cov: 31)

Exomes 𝑓: 0.86 ( 88556 hom. )

Consequence

CD209
NM_021155.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.88

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD209	NM_021155.4 linkuse as main transcript	c.*2797C>T		3_prime_UTR_variant	7/7	ENST00000315599.12	NP_066978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD209	ENST00000315599.12 linkuse as main transcript	c.*2797C>T		3_prime_UTR_variant	7/7	1	NM_021155.4	ENSP00000315477	P2	Q9NNX6-1

Frequencies

GnomAD3 genomes

AF:

0.811

AC:

123262

AN:

151978

Hom.:

50606

Cov.:

show subpopulations

Gnomad AFR

AF:

0.683

Gnomad AMI

AF:

0.715

Gnomad AMR

AF:

0.861

Gnomad ASJ

AF:

0.852

Gnomad EAS

AF:

0.697

Gnomad SAS

AF:

0.832

Gnomad FIN

AF:

0.864

Gnomad MID

AF:

0.918

Gnomad NFE

AF:

0.875

Gnomad OTH

AF:

0.826

GnomAD4 exome

AF:

0.858

AC:

205534

AN:

239522

Hom.:

88556

Cov.:

AF XY:

0.857

AC XY:

110621

AN XY:

129008

show subpopulations

Gnomad4 AFR exome

AF:

0.678

Gnomad4 AMR exome

AF:

0.860

Gnomad4 ASJ exome

AF:

0.866

Gnomad4 EAS exome

AF:

0.733

Gnomad4 SAS exome

AF:

0.851

Gnomad4 FIN exome

AF:

0.870

Gnomad4 NFE exome

AF:

0.877

Gnomad4 OTH exome

AF:

0.853

GnomAD4 genome

AF:

0.811

AC:

123358

AN:

152096

Hom.:

50648

Cov.:

AF XY:

0.809

AC XY:

60199

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.683

Gnomad4 AMR

AF:

0.861

Gnomad4 ASJ

AF:

0.852

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.833

Gnomad4 FIN

AF:

0.864

Gnomad4 NFE

AF:

0.875

Gnomad4 OTH

AF:

0.828

Alfa

AF:

0.861

Hom.:

52023

Bravo

AF:

0.803

Asia WGS

AF:

0.778

AC:

2705

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.41

DANN

Benign

0.61

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over