chr22-20316129-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033257.4(DGCR6L):c.362G>A(p.Arg121Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,610,024 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033257.4 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 |
---|---|---|---|---|---|---|---|
DGCR6L | NM_033257.4 | c.362G>A | p.Arg121Gln | missense_variant | 3/5 | ENST00000248879.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR6L | ENST00000248879.8 | c.362G>A | p.Arg121Gln | missense_variant | 3/5 | 1 | NM_033257.4 | P1 | |
DGCR6L | ENST00000443409.1 | c.272-653G>A | intron_variant, NMD_transcript_variant | 1 | |||||
DGCR6L | ENST00000405465.3 | c.259-653G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000818 AC: 20AN: 244412Hom.: 1 AF XY: 0.0000527 AC XY: 7AN XY: 132788
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1457808Hom.: 1 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 725034
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2021 | The c.362G>A (p.R121Q) alteration is located in exon 3 (coding exon 3) of the DGCR6L gene. This alteration results from a G to A substitution at nucleotide position 362, causing the arginine (R) at amino acid position 121 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