rs142126065
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_031407.7(HUWE1):c.3663G>A(p.Ser1221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,209,598 control chromosomes in the GnomAD database, including 3 homozygotes. There are 424 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_031407.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HUWE1 | NM_031407.7 | c.3663G>A | p.Ser1221= | synonymous_variant | 32/84 | ENST00000262854.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HUWE1 | ENST00000262854.11 | c.3663G>A | p.Ser1221= | synonymous_variant | 32/84 | 1 | NM_031407.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000973 AC: 109AN: 111974Hom.: 0 Cov.: 24 AF XY: 0.00105 AC XY: 36AN XY: 34150
GnomAD3 exomes AF: 0.000644 AC: 118AN: 183335Hom.: 0 AF XY: 0.000885 AC XY: 60AN XY: 67785
GnomAD4 exome AF: 0.00104 AC: 1136AN: 1097570Hom.: 3 Cov.: 30 AF XY: 0.00107 AC XY: 388AN XY: 362934
GnomAD4 genome ? AF: 0.000973 AC: 109AN: 112028Hom.: 0 Cov.: 24 AF XY: 0.00105 AC XY: 36AN XY: 34214
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:5
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 09, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 22, 2015 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 30, 2017 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 24, 2018 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at