19-7745597-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_021155.4(CD209):c.669G>A(p.Lys223Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000524 in 634,964 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00025 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00061 ( 3 hom. )
Consequence
CD209
NM_021155.4 synonymous
NM_021155.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.854
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 19-7745597-C-T is Benign according to our data. Variant chr19-7745597-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649174.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.854 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD209 | ENST00000315599.12 | c.669G>A | p.Lys223Lys | synonymous_variant | Exon 4 of 7 | 1 | NM_021155.4 | ENSP00000315477.6 | ||
ENSG00000288669 | ENST00000678003.1 | n.66G>A | non_coding_transcript_exon_variant | Exon 1 of 13 | ENSP00000504497.1 |
Frequencies
GnomAD3 genomes AF: 0.000246 AC: 37AN: 150592Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000189 AC: 40AN: 211406Hom.: 0 AF XY: 0.000198 AC XY: 23AN XY: 116180
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GnomAD4 exome AF: 0.000611 AC: 296AN: 484258Hom.: 3 Cov.: 0 AF XY: 0.000857 AC XY: 223AN XY: 260186
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GnomAD4 genome AF: 0.000246 AC: 37AN: 150706Hom.: 0 Cov.: 31 AF XY: 0.000353 AC XY: 26AN XY: 73658
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
CD209: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at