11-118384947-TAAAAAAAAAAAAA-TAAAAAAAAAAA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000252108.8(UBE4A):c.2412+3_2412+4delAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,007,182 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000252108.8 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBE4A | NM_001204077.2 | c.2412+22_2412+23delAA | intron_variant | Intron 15 of 19 | ENST00000252108.8 | NP_001191006.1 | ||
UBE4A | NM_004788.4 | c.2433+22_2433+23delAA | intron_variant | Intron 15 of 19 | NP_004779.2 | |||
LOC100131626 | NR_046369.1 | n.232-3389_232-3388delTT | intron_variant | Intron 3 of 3 | ||||
LOC100131626 | NR_046370.1 | n.232-3442_232-3441delTT | intron_variant | Intron 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBE4A | ENST00000252108.8 | c.2412+3_2412+4delAA | splice_region_variant, intron_variant | Intron 15 of 19 | 1 | NM_001204077.2 | ENSP00000252108.4 | |||
UBE4A | ENST00000431736.6 | c.2433+3_2433+4delAA | splice_region_variant, intron_variant | Intron 15 of 19 | 1 | ENSP00000387362.2 | ||||
UBE4A | ENST00000545354.1 | c.828+3_828+4delAA | splice_region_variant, intron_variant | Intron 6 of 10 | 2 | ENSP00000438918.1 |
Frequencies
GnomAD3 genomes AF: 0.00204 AC: 162AN: 79398Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.191 AC: 15984AN: 83660Hom.: 1 AF XY: 0.191 AC XY: 8654AN XY: 45246
GnomAD4 exome AF: 0.151 AC: 139794AN: 927796Hom.: 0 AF XY: 0.152 AC XY: 71360AN XY: 470852
GnomAD4 genome AF: 0.00204 AC: 162AN: 79386Hom.: 0 Cov.: 29 AF XY: 0.00228 AC XY: 86AN XY: 37712
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at