Variant rs11465413 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.*1974T>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.13 in 820,240 control chromosomes in the GnomAD database, including 10,771 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 0.18 ( 4237 hom., cov: 32)

Exomes 𝑓: 0.12 ( 6534 hom. )

Consequence

CD209
NM_021155.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.64

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:

ENSG00000288669 (HGNC:):

ENSG00000288669 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=-0.66).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 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.*1974T>A		3_prime_UTR_variant	7/7	ENST00000315599.12	NP_066978.1	Q9NNX6-1B2R907

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD209	ENST00000315599 linkuse as main transcript	c.*1974T>A		3_prime_UTR_variant	7/7	1	NM_021155.4	ENSP00000315477.6		Q9NNX6-1
ENSG00000288669	ENST00000678003.1 linkuse as main transcript	n.*290+502T>A		intron_variant				ENSP00000504497.1		A0A7I2YQT4

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27296

AN:

152116

Hom.:

4206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.417

Gnomad AMI

AF:

0.0659

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.0391

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0844

Gnomad OTH

AF:

0.151

GnomAD4 exome

AF:

0.118

AC:

78980

AN:

668004

Hom.:

6534

Cov.:

AF XY:

0.119

AC XY:

42718

AN XY:

358960

show subpopulations

Gnomad4 AFR exome

AF:

0.464

Gnomad4 AMR exome

AF:

0.0685

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.102

Gnomad4 SAS exome

AF:

0.190

Gnomad4 FIN exome

AF:

0.0442

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.128

GnomAD4 genome

AF:

0.180

AC:

27375

AN:

152236

Hom.:

4237

Cov.:

AF XY:

0.177

AC XY:

13150

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.418

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.104

Gnomad4 EAS

AF:

0.115

Gnomad4 SAS

AF:

0.186

Gnomad4 FIN

AF:

0.0391

Gnomad4 NFE

AF:

0.0844

Gnomad4 OTH

AF:

0.150

Alfa

AF:

0.131

Hom.:

316

Bravo

AF:

0.192

Asia WGS

AF:

0.162

AC:

563

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

2.2

DANN

Benign

0.64

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