chr22-19041067-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005137.3(DGCR2):c.1387G>T(p.Asp463Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,601,842 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. D463E) has been classified as Uncertain significance.
Frequency
Consequence
NM_005137.3 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 |
---|---|---|---|---|---|---|---|
DGCR2 | NM_005137.3 | c.1387G>T | p.Asp463Tyr | missense_variant | 9/10 | ENST00000263196.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR2 | ENST00000263196.12 | c.1387G>T | p.Asp463Tyr | missense_variant | 9/10 | 1 | NM_005137.3 | P1 | |
DGCR2 | ENST00000389262.8 | c.*958G>T | 3_prime_UTR_variant, NMD_transcript_variant | 10/11 | 1 | ||||
DGCR2 | ENST00000537045.5 | c.1264G>T | p.Asp422Tyr | missense_variant | 8/9 | 2 | |||
DGCR2 | ENST00000467659.1 | n.1165G>T | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000950 AC: 23AN: 242002Hom.: 0 AF XY: 0.0000690 AC XY: 9AN XY: 130354
GnomAD4 exome AF: 0.000103 AC: 149AN: 1449638Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 77AN XY: 719638
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2022 | The c.1387G>T (p.D463Y) alteration is located in exon 9 (coding exon 9) of the DGCR2 gene. This alteration results from a G to T substitution at nucleotide position 1387, causing the aspartic acid (D) at amino acid position 463 to be replaced by a tyrosine (Y). 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