Genetic Variant NM_021155.4:c.*2797C>G (chr19-7740242-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_021155.4(CD209):c.*2797C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000417 in 239,864 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)

Exomes 𝑓: 0.0000042 ( 0 hom. )

Consequence

CD209
NM_021155.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.88

Publications

21 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021155.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD209	NM_021155.4	MANE Select	c.*2797C>G	3_prime_UTR	Exon 7 of 7	NP_066978.1	Q9NNX6-1
CD209	NM_001144897.2		c.*2797C>G	3_prime_UTR	Exon 7 of 7	NP_001138369.1	Q9NNX6-2
CD209	NM_001144896.2		c.*2797C>G	3_prime_UTR	Exon 6 of 6	NP_001138368.1	Q9NNX6-6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD209	ENST00000315599.12	TSL:1 MANE Select	c.*2797C>G	3_prime_UTR	Exon 7 of 7	ENSP00000315477.6	Q9NNX6-1
ENSG00000288669	ENST00000678003.1		n.*290+1325C>G	intron	N/A	ENSP00000504497.1	A0A7I2YQT4
ENSG00000288669	ENST00000676543.1		n.70+5276C>G	intron	N/A	ENSP00000503143.1	A0A7I2V366

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000417

AC:

AN:

239864

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

129160

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6646

American (AMR)

AF:

0.00

AC:

AN:

8218

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6630

East Asian (EAS)

AF:

0.00

AC:

AN:

11844

South Asian (SAS)

AF:

0.00

AC:

AN:

32632

European-Finnish (FIN)

AF:

0.00

AC:

AN:

14298

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1006

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

145462

Other (OTH)

AF:

0.0000762

AC:

AN:

13128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

67976

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.26

(source)

DANN

Benign

0.15

PhyloP100

-2.9

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over