rs1018783
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_080911.3(UNG):c.132+241T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 1,368,336 control chromosomes in the GnomAD database, including 24,297 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4665 hom., cov: 33)
Exomes 𝑓: 0.17 ( 19632 hom. )
Consequence
UNG
NM_080911.3 intron
NM_080911.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.503
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 12-109098052-T-A is Benign according to our data. Variant chr12-109098052-T-A is described in ClinVar as [Benign]. Clinvar id is 1258409.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNG | NM_080911.3 | c.132+241T>A | intron_variant | ENST00000242576.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNG | ENST00000242576.7 | c.132+241T>A | intron_variant | 1 | NM_080911.3 | P1 | |||
UNG | ENST00000540158.1 | n.133+241T>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.227 AC: 34456AN: 151714Hom.: 4662 Cov.: 33
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GnomAD4 exome AF: 0.174 AC: 212036AN: 1216504Hom.: 19632 AF XY: 0.173 AC XY: 101635AN XY: 586544
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GnomAD4 genome ? AF: 0.227 AC: 34486AN: 151832Hom.: 4665 Cov.: 33 AF XY: 0.223 AC XY: 16565AN XY: 74250
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 06, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at