22-18910222-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005675.6(DGCR6):c.322C>G(p.Arg108Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R108Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_005675.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR6 | NM_005675.6 | c.322C>G | p.Arg108Gly | missense_variant | 3/5 | ENST00000331444.12 | |
DGCR6 | XM_047441510.1 | c.115C>G | p.Arg39Gly | missense_variant | 3/5 | ||
DGCR6 | XM_047441509.1 | c.441C>G | p.Ala147= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR6 | ENST00000331444.12 | c.322C>G | p.Arg108Gly | missense_variant | 3/5 | 1 | NM_005675.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 5252Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 exomes AF: 0.0000333 AC: 8AN: 240030Hom.: 0 AF XY: 0.0000459 AC XY: 6AN XY: 130826
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 51174Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 28260
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 5252Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2186
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2024 | The c.322C>G (p.R108G) alteration is located in exon 3 (coding exon 3) of the DGCR6 gene. This alteration results from a C to G substitution at nucleotide position 322, causing the arginine (R) at amino acid position 108 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at