rs76391872
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_080911.3(UNG):āc.759C>Gā(p.Leu253=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00341 in 1,613,926 control chromosomes in the GnomAD database, including 176 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.019 ( 94 hom., cov: 31)
Exomes š: 0.0018 ( 82 hom. )
Consequence
UNG
NM_080911.3 synonymous
NM_080911.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.338
Genes affected
UNG (HGNC:12572): (uracil DNA glycosylase) This gene encodes one of several uracil-DNA glycosylases. One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosylic bond and initiating the base-excision repair (BER) pathway. Uracil bases occur from cytosine deamination or misincorporation of dUMP residues. Alternative promoter usage and splicing of this gene leads to two different isoforms: the mitochondrial UNG1 and the nuclear UNG2. The UNG2 term was used as a previous symbol for the CCNO gene (GeneID 10309), which has been confused with this gene, in the literature and some databases. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 12-109103569-C-G is Benign according to our data. Variant chr12-109103569-C-G is described in ClinVar as [Benign]. Clinvar id is 306977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.338 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0645 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNG | NM_080911.3 | c.759C>G | p.Leu253= | synonymous_variant | 6/7 | ENST00000242576.7 | |
UNG | NM_003362.4 | c.732C>G | p.Leu244= | synonymous_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNG | ENST00000242576.7 | c.759C>G | p.Leu253= | synonymous_variant | 6/7 | 1 | NM_080911.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2866AN: 152072Hom.: 94 Cov.: 31
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GnomAD3 exomes AF: 0.00456 AC: 1147AN: 251346Hom.: 37 AF XY: 0.00321 AC XY: 436AN XY: 135854
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GnomAD4 exome AF: 0.00180 AC: 2631AN: 1461736Hom.: 82 Cov.: 32 AF XY: 0.00153 AC XY: 1110AN XY: 727164
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GnomAD4 genome ? AF: 0.0189 AC: 2873AN: 152190Hom.: 94 Cov.: 31 AF XY: 0.0176 AC XY: 1313AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hyper-IgM syndrome type 5 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at