3-49110321-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001199161.2(USP19):c.3901G>A(p.Glu1301Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,603,972 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001199161.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000455 AC: 11AN: 241988Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 131060
GnomAD4 exome AF: 0.000104 AC: 151AN: 1451664Hom.: 0 Cov.: 31 AF XY: 0.0000777 AC XY: 56AN XY: 720910
GnomAD4 genome AF: 0.000217 AC: 33AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3895G>A (p.E1299K) alteration is located in exon 26 (coding exon 25) of the USP19 gene. This alteration results from a G to A substitution at nucleotide position 3895, causing the glutamic acid (E) at amino acid position 1299 to be replaced by a lysine (K). 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