chrX-133026159-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_031907.3(USP26):c.2062G>A(p.Asp688Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,208,345 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_031907.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000907 AC: 1AN: 110274Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32518
GnomAD3 exomes AF: 0.0000329 AC: 6AN: 182468Hom.: 0 AF XY: 0.0000297 AC XY: 2AN XY: 67428
GnomAD4 exome AF: 0.0000137 AC: 15AN: 1098071Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 8AN XY: 363485
GnomAD4 genome AF: 0.00000907 AC: 1AN: 110274Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32518
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | USP26: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at