chr22-18910223-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005675.6(DGCR6):c.323G>A(p.Arg108Gln) 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. R108G) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR6 | NM_005675.6 | c.323G>A | p.Arg108Gln | missense_variant | 3/5 | ENST00000331444.12 | |
DGCR6 | XM_047441509.1 | c.442G>A | p.Gly148Ser | missense_variant | 4/4 | ||
DGCR6 | XM_047441510.1 | c.116G>A | p.Arg39Gln | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR6 | ENST00000331444.12 | c.323G>A | p.Arg108Gln | missense_variant | 3/5 | 1 | NM_005675.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 exomes AF: 0.0000998 AC: 24AN: 240592Hom.: 0 AF XY: 0.0000687 AC XY: 9AN XY: 131046
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 52326Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 28882
GnomAD4 genome ? Cov.: 0
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.323G>A (p.R108Q) alteration is located in exon 3 (coding exon 3) of the DGCR6 gene. This alteration results from a G to A substitution at nucleotide position 323, causing the arginine (R) at amino acid position 108 to be replaced by a glutamine (Q). 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