rs149435515
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_031407.7(HUWE1):c.147C>T(p.Cys49=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00014 in 1,180,626 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 38 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 1/1 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, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HUWE1 | NM_031407.7 | c.147C>T | p.Cys49= | splice_region_variant, synonymous_variant | 6/84 | ENST00000262854.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HUWE1 | ENST00000262854.11 | c.147C>T | p.Cys49= | splice_region_variant, synonymous_variant | 6/84 | 1 | NM_031407.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000715 AC: 8AN: 111844Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34020
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183193Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67705
GnomAD4 exome AF: 0.000147 AC: 157AN: 1068782Hom.: 0 Cov.: 28 AF XY: 0.000110 AC XY: 37AN XY: 336984
GnomAD4 genome ? AF: 0.0000715 AC: 8AN: 111844Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34020
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 06, 2015 | - - |
HUWE1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 22, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at