5-172769719-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004417.4(DUSP1):c.589G>A(p.Ala197Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,614,164 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A197S) has been classified as Uncertain significance.
Frequency
Consequence
NM_004417.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152272Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251494Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135922
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461892Hom.: 0 Cov.: 36 AF XY: 0.00000963 AC XY: 7AN XY: 727248
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152272Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.589G>A (p.A197T) alteration is located in exon 3 (coding exon 3) of the DUSP1 gene. This alteration results from a G to A substitution at nucleotide position 589, causing the alanine (A) at amino acid position 197 to be replaced by a threonine (T). 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