2-96143990-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004418.4(DUSP2):c.778G>A(p.Gly260Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,613,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004418.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000919 AC: 23AN: 250328Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135532
GnomAD4 exome AF: 0.000142 AC: 208AN: 1461462Hom.: 0 Cov.: 32 AF XY: 0.000151 AC XY: 110AN XY: 727038
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.778G>A (p.G260S) alteration is located in exon 4 (coding exon 4) of the DUSP2 gene. This alteration results from a G to A substitution at nucleotide position 778, causing the glycine (G) at amino acid position 260 to be replaced by a serine (S). 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