rs11465413

Variant names:

• chr19-7741065-A-T
• rs11465413
• NM_021155.4:c.*1974T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.64
• Publications: 10 publications found

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]

ENSG00000288669 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CD209	NM_021155.4	c.*1974T>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000315599.12	NP_066978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD209	ENST00000315599.12	c.*1974T>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_021155.4	ENSP00000315477.6
ENSG00000288669	ENST00000678003.1	n.*290+502T>A		intron_variant	Intron 2 of 12			ENSP00000504497.1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27296 AN: 152116 Hom.: 4206 Cov.: 32

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.: 9 AF XY: 0.119 AC XY: 42718 AN XY: 358960

African (AFR) AF: 0.464 AC: 8995 AN: 19374

American (AMR) AF: 0.0685 AC: 2487 AN: 36330

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 2018 AN: 18300

East Asian (EAS) AF: 0.102 AC: 3298 AN: 32486

South Asian (SAS) AF: 0.190 AC: 12876 AN: 67644

European-Finnish (FIN) AF: 0.0442 AC: 2093 AN: 47378

Middle Eastern (MID) AF: 0.136 AC: 546 AN: 4014

European-Non Finnish (NFE) AF: 0.104 AC: 42490 AN: 409906

Other (OTH) AF: 0.128 AC: 4177 AN: 32572

GnomAD4 genome AF: 0.180 AC: 27375 AN: 152236 Hom.: 4237 Cov.: 32 AF XY: 0.177 AC XY: 13150 AN XY: 74436

African (AFR) AF: 0.418 AC: 17343 AN: 41496

American (AMR) AF: 0.105 AC: 1610 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3472

East Asian (EAS) AF: 0.115 AC: 597 AN: 5184

South Asian (SAS) AF: 0.186 AC: 900 AN: 4830

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10618

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5743 AN: 68016

Other (OTH) AF: 0.150 AC: 318 AN: 2114

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
PhyloP100		3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11465413; hg19: chr19-7805951; COSMIC: COSV52654377; COSMIC: COSV52654377;