chrX-53627887-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_031407.7(HUWE1):c.1243-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000915 in 1,092,741 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_031407.7 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HUWE1 | NM_031407.7 | c.1243-8C>T | splice_region_variant, intron_variant | Intron 15 of 83 | ENST00000262854.11 | NP_113584.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181468Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66024
GnomAD4 exome AF: 0.00000915 AC: 10AN: 1092741Hom.: 0 Cov.: 29 AF XY: 0.0000112 AC XY: 4AN XY: 358309
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 30, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at