19-7745604-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_021155.4(CD209):c.662G>A(p.Arg221Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00318 in 617,018 control chromosomes in the GnomAD database, including 7 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 (no stars).
Frequency
Consequence
NM_021155.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD209 | ENST00000315599.12 | c.662G>A | p.Arg221Gln | missense_variant | Exon 4 of 7 | 1 | NM_021155.4 | ENSP00000315477.6 | ||
ENSG00000288669 | ENST00000678003.1 | n.59G>A | non_coding_transcript_exon_variant | Exon 1 of 13 | ENSP00000504497.1 |
Frequencies
GnomAD3 genomes AF: 0.0127 AC: 1778AN: 140142Hom.: 5 Cov.: 30
GnomAD3 exomes AF: 0.000504 AC: 113AN: 223996Hom.: 2 AF XY: 0.000259 AC XY: 32AN XY: 123446
GnomAD4 exome AF: 0.000390 AC: 186AN: 476752Hom.: 2 Cov.: 0 AF XY: 0.000370 AC XY: 95AN XY: 256682
GnomAD4 genome AF: 0.0127 AC: 1776AN: 140266Hom.: 5 Cov.: 30 AF XY: 0.0121 AC XY: 830AN XY: 68510
ClinVar
Submissions by phenotype
CD209-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at