19-10567240-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001800.4(CDKN2D):c.319G>A(p.Gly107Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,032 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001800.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKN2D | NM_001800.4 | c.319G>A | p.Gly107Arg | missense_variant | Exon 2 of 2 | ENST00000393599.3 | NP_001791.1 | |
CDKN2D | NM_079421.3 | c.319G>A | p.Gly107Arg | missense_variant | Exon 3 of 3 | NP_524145.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251438Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135906
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461866Hom.: 1 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727236
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.319G>A (p.G107R) alteration is located in exon 2 (coding exon 2) of the CDKN2D gene. This alteration results from a G to A substitution at nucleotide position 319, causing the glycine (G) at amino acid position 107 to be replaced by an arginine (R). 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