chr15-25339119-ATTTTG-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_130839.5(UBE3A):​c.*13_*17del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,429,850 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000022 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000023 ( 0 hom. )

Consequence

UBE3A
NM_130839.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter U:1B:1

Conservation

PhyloP100: 0.720
Variant links:
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.

BP6
Variant 15-25339119-ATTTTG-A is Benign according to our data. Variant chr15-25339119-ATTTTG-A is described in ClinVar as [Likely_benign]. Clinvar id is 156147.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 30 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UBE3ANM_130839.5 linkuse as main transcriptc.*13_*17del 3_prime_UTR_variant 13/13 ENST00000648336.2
SNHG14NR_146177.1 linkuse as main transcriptn.18393-52462_18393-52458del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UBE3AENST00000648336.2 linkuse as main transcriptc.*13_*17del 3_prime_UTR_variant 13/13 NM_130839.5 P1Q05086-3
SNHG14ENST00000656420.1 linkuse as main transcriptn.5456+60250_5456+60254del intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0000219
AC:
3
AN:
136802
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000323
Gnomad OTH
AF:
0.000526
GnomAD4 exome
AF:
0.0000232
AC:
30
AN:
1293048
Hom.:
0
AF XY:
0.0000284
AC XY:
18
AN XY:
632732
show subpopulations
Gnomad4 AFR exome
AF:
0.0000726
Gnomad4 AMR exome
AF:
0.0000440
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000586
Gnomad4 SAS exome
AF:
0.0000169
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000234
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000219
AC:
3
AN:
136802
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
66620
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000323
Gnomad4 OTH
AF:
0.000526
Bravo
AF:
0.0000302

ClinVar

Significance: Likely benign
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Angelman syndrome Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingBaylor GeneticsFeb 14, 2014possible diagnosis of Angelman syndrome -
not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJul 14, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs587782926; hg19: chr15-25584266; API