chr22-20086622-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_022720.7(DGCR8):c.659C>T(p.Thr220Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,612,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022720.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR8 | NM_022720.7 | c.659C>T | p.Thr220Met | missense_variant | 2/14 | ENST00000351989.8 | |
DGCR8 | NM_001190326.2 | c.659C>T | p.Thr220Met | missense_variant | 2/13 | ||
DGCR8 | XM_047441418.1 | c.659C>T | p.Thr220Met | missense_variant | 2/14 | ||
DGCR8 | XM_047441419.1 | c.659C>T | p.Thr220Met | missense_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR8 | ENST00000351989.8 | c.659C>T | p.Thr220Met | missense_variant | 2/14 | 1 | NM_022720.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249840Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135150
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460338Hom.: 0 Cov.: 32 AF XY: 0.00000826 AC XY: 6AN XY: 726512
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74402
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at