chr22-19041065-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005137.3(DGCR2):c.1389C>A(p.Asp463Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 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. D463Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_005137.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR2 | NM_005137.3 | c.1389C>A | p.Asp463Glu | missense_variant | 9/10 | ENST00000263196.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR2 | ENST00000263196.12 | c.1389C>A | p.Asp463Glu | missense_variant | 9/10 | 1 | NM_005137.3 | P1 | |
DGCR2 | ENST00000389262.8 | c.*960C>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/11 | 1 | ||||
DGCR2 | ENST00000537045.5 | c.1266C>A | p.Asp422Glu | missense_variant | 8/9 | 2 | |||
DGCR2 | ENST00000467659.1 | n.1167C>A | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2022 | The c.1389C>A (p.D463E) alteration is located in exon 9 (coding exon 9) of the DGCR2 gene. This alteration results from a C to A substitution at nucleotide position 1389, causing the aspartic acid (D) at amino acid position 463 to be replaced by a glutamic acid (E). 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