X-53534126-T-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_031407.7(HUWE1):āc.12903A>Cā(p.Thr4301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000906 in 110,371 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. T4301T) has been classified as Benign.
Frequency
Consequence
NM_031407.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HUWE1 | NM_031407.7 | c.12903A>C | p.Thr4301= | synonymous_variant | 83/84 | ENST00000262854.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HUWE1 | ENST00000262854.11 | c.12903A>C | p.Thr4301= | synonymous_variant | 83/84 | 1 | NM_031407.7 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000906 AC: 1AN: 110371Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32539
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000237 AC: 26AN: 1097592Hom.: 0 Cov.: 42 AF XY: 0.0000331 AC XY: 12AN XY: 362960
GnomAD4 genome AF: 0.00000906 AC: 1AN: 110371Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32539
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2023 | This variant is present in population databases (rs477171, gnomAD 0.1%). This sequence change affects codon 4301 of the HUWE1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the HUWE1 protein. This variant has not been reported in the literature in individuals affected with HUWE1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at