chr19-7745880-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021155.4(CD209):c.386G>A(p.Arg129Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000294 in 1,601,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021155.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD209 | NM_021155.4 | c.386G>A | p.Arg129Gln | missense_variant | 4/7 | ENST00000315599.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD209 | ENST00000315599.12 | c.386G>A | p.Arg129Gln | missense_variant | 4/7 | 1 | NM_021155.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000354 AC: 5AN: 141142Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000561 AC: 14AN: 249382Hom.: 1 AF XY: 0.0000519 AC XY: 7AN XY: 134934
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1459790Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 726212
GnomAD4 genome ? AF: 0.0000354 AC: 5AN: 141268Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 68804
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | CD209: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at