rs150573868
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_003355.3(UCP2):c.816-2A>G variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,609,850 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_003355.3 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UCP2 | NM_003355.3 | c.816-2A>G | splice_acceptor_variant, intron_variant | Intron 7 of 7 | ENST00000663595.2 | NP_003346.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UCP2 | ENST00000663595.2 | c.816-2A>G | splice_acceptor_variant, intron_variant | Intron 7 of 7 | NM_003355.3 | ENSP00000499695.1 | ||||
UCP2 | ENST00000310473.9 | c.816-2A>G | splice_acceptor_variant, intron_variant | Intron 8 of 8 | 1 | ENSP00000312029.3 | ||||
UCP2 | ENST00000536983.5 | c.635-2A>G | splice_acceptor_variant, intron_variant | Intron 6 of 6 | 5 | ENSP00000441147.1 | ||||
UCP2 | ENST00000544615.5 | n.735-2A>G | splice_acceptor_variant, intron_variant | Intron 4 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000922 AC: 14AN: 151896Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000127 AC: 31AN: 243374Hom.: 0 AF XY: 0.000114 AC XY: 15AN XY: 131572
GnomAD4 exome AF: 0.000110 AC: 160AN: 1457954Hom.: 0 Cov.: 31 AF XY: 0.000103 AC XY: 75AN XY: 724998
GnomAD4 genome AF: 0.0000922 AC: 14AN: 151896Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74174
ClinVar
Submissions by phenotype
not provided Uncertain:2
The UCP2 c.816-2A>G variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs150573868), ClinVar (classified as a VUS by Genetic Services Laboratory, University of Chicago). The variant was identified in control databases in 35 of 274688 chromosomes at a frequency of 0.000127 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 34 of 124762 chromosomes (freq: 0.000273), Other in 1 of 7090 chromosomes (freq: 0.000141), while the variant was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), and South Asian populations. The c.816-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
This sequence change affects an acceptor splice site in intron 7 of the UCP2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), however the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in UCP2 cause disease. This variant is present in population databases (rs150573868, gnomAD 0.03%). Disruption of this splice site has been observed in individual(s) with congenital hyperinsulinism (PMID: 27967291). ClinVar contains an entry for this variant (Variation ID: 212542). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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. -
not specified Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at