Variant chr11-118384947-T-TAAAAAAAAAAAAAAAAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001204077.2(UBE4A):c.2412+5_2412+23dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 29)

Failed GnomAD Quality Control

Consequence

UBE4A
NM_001204077.2 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.09

Variant links:

Genes affected

UBE4A (HGNC:12499): (ubiquitination factor E4A) This gene encodes a member of the U-box ubiquitin ligase family. The encoded protein is involved in multiubiquitin chain assembly and plays a critical role in chromosome condensation and separation through the polyubiquitination of securin. Autoantibodies against the encoded protein may be markers for scleroderma and Crohn's disease. A pseudogene of this gene is located on the long arm of chromosome 3. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

UBE4A links:

LOC100131626 (HGNC:):

LOC100131626 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
UBE4A	NM_001204077.2 linkuse as main transcript	c.2412+5_2412+23dup	splice_region_variant, intron_variant	ENST00000252108.8
LOC100131626	NR_046370.1 linkuse as main transcript	n.232-3441_232-3440insTTTTTTTTTTTTTTTTTTT	intron_variant, non_coding_transcript_variant
UBE4A	NM_004788.4 linkuse as main transcript	c.2433+5_2433+23dup	splice_region_variant, intron_variant
LOC100131626	NR_046369.1 linkuse as main transcript	n.232-3388_232-3387insTTTTTTTTTTTTTTTTTTT	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
UBE4A	ENST00000252108.8 linkuse as main transcript	c.2412+5_2412+23dup	splice_region_variant, intron_variant	1	NM_001204077.2	P1	Q14139-1
UBE4A	ENST00000431736.6 linkuse as main transcript	c.2433+5_2433+23dup	splice_region_variant, intron_variant	1			Q14139-2
UBE4A	ENST00000545354.1 linkuse as main transcript	c.828+5_828+23dup	splice_region_variant, intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

79516

Hom.:

Cov.:

FAILED QC

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

79516

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

37764

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:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over