6-14135163-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004233.4(CD83):c.545G>A(p.Arg182Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00249 in 1,613,782 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004233.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD83 | NM_004233.4 | c.545G>A | p.Arg182Gln | missense_variant | 5/5 | ENST00000379153.4 | |
CD83 | NM_001040280.3 | c.542G>A | p.Arg181Gln | missense_variant | 5/5 | ||
CD83 | NM_001251901.1 | c.368G>A | p.Arg123Gln | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD83 | ENST00000379153.4 | c.545G>A | p.Arg182Gln | missense_variant | 5/5 | 1 | NM_004233.4 | P1 | |
CD83 | ENST00000612003.4 | c.368G>A | p.Arg123Gln | missense_variant | 5/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0135 AC: 2058AN: 152148Hom.: 48 Cov.: 33
GnomAD3 exomes AF: 0.00355 AC: 892AN: 251472Hom.: 21 AF XY: 0.00261 AC XY: 355AN XY: 135908
GnomAD4 exome AF: 0.00134 AC: 1961AN: 1461518Hom.: 47 Cov.: 30 AF XY: 0.00111 AC XY: 804AN XY: 727088
GnomAD4 genome ? AF: 0.0135 AC: 2056AN: 152264Hom.: 48 Cov.: 33 AF XY: 0.0132 AC XY: 985AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at