GeneBe

chr11-118384947-T-TAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAA

Position:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000252108.8(UBE4A):​c.2412+23_2412+24insAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)

Consequence

UBE4A
ENST00000252108.8 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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UBE4ANM_001204077.2 linkuse as main transcriptc.2412+23_2412+24insAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA splice_region_variant, intron_variant ENST00000252108.8 NP_001191006.1
LOC100131626NR_046370.1 linkuse as main transcriptn.232-3441_232-3440insTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTT intron_variant, non_coding_transcript_variant
UBE4ANM_004788.4 linkuse as main transcriptc.2433+23_2433+24insAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA splice_region_variant, intron_variant NP_004779.2
LOC100131626NR_046369.1 linkuse as main transcriptn.232-3388_232-3387insTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTT intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UBE4AENST00000252108.8 linkuse as main transcriptc.2412+23_2412+24insAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA splice_region_variant, intron_variant 1 NM_001204077.2 ENSP00000252108 P1Q14139-1
UBE4AENST00000431736.6 linkuse as main transcriptc.2433+23_2433+24insAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA splice_region_variant, intron_variant 1 ENSP00000387362 Q14139-2
UBE4AENST00000545354.1 linkuse as main transcriptc.828+23_828+24insAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA splice_region_variant, intron_variant 2 ENSP00000438918

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
29

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.

Other links and lift over

dbSNP: rs370025001; hg19: chr11-118255662; API