chr15-25339114-G-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_130839.5(UBE3A):c.*23C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0085 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
UBE3A
NM_130839.5 3_prime_UTR
NM_130839.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00
Genes affected
UBE3A (HGNC:12496): (ubiquitin protein ligase E3A) This gene encodes an E3 ubiquitin-protein ligase, part of the ubiquitin protein degradation system. This imprinted gene is maternally expressed in brain and biallelically expressed in other tissues. Maternally inherited deletion of this gene causes Angelman Syndrome, characterized by severe motor and intellectual retardation, ataxia, hypotonia, epilepsy, absence of speech, and characteristic facies. The protein also interacts with the E6 protein of human papillomavirus types 16 and 18, resulting in ubiquitination and proteolysis of tumor protein p53. Alternative splicing of this gene results in three transcript variants encoding three isoforms with different N-termini. Additional transcript variants have been described, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
SNHG14 (HGNC:37462): (small nucleolar RNA host gene 14) This gene is located within the Prader-Willi critical region and produces a long, spliced paternally-imprinted RNA that initiates within a common upstream promoter region shared by the SNRPN (small nuclear ribonucleoprotein polypeptide N) and SNURF genes. This transcript serves as a host RNA for the small nucleolar RNA, C/D box 115 and 116 clusters. This RNA extends in antisense into the region of the ubiquitin protein ligase E3A gene (UBE3A), and is thought to regulate imprinted expression of UBE3A in the brain. This transcript undergoes extensive alternative splicing, and may initiate and terminate at multiple locations within this genomic region. The full-length structure of all splice forms is not determined. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 15-25339114-G-T is Benign according to our data. Variant chr15-25339114-G-T is described in ClinVar as [Benign]. Clinvar id is 1292518.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE3A | NM_130839.5 | c.*23C>A | 3_prime_UTR_variant | 13/13 | ENST00000648336.2 | ||
SNHG14 | NR_146177.1 | n.18393-52482G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE3A | ENST00000648336.2 | c.*23C>A | 3_prime_UTR_variant | 13/13 | NM_130839.5 | P1 | |||
SNHG14 | ENST00000656420.1 | n.5456+60230G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 23AN: 135732Hom.: 0 Cov.: 32 FAILED QC
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GnomAD3 exomes AF: 0.0184 AC: 2035AN: 110544Hom.: 0 AF XY: 0.0166 AC XY: 1026AN XY: 61818
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00851 AC: 10379AN: 1219996Hom.: 0 Cov.: 30 AF XY: 0.00938 AC XY: 5568AN XY: 593630
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000169 AC: 23AN: 135826Hom.: 0 Cov.: 32 AF XY: 0.000197 AC XY: 13AN XY: 65880
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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 | Mar 06, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at