11-118384947-TAAAAAAAAAAAAA-TAAAAAAAAAA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001204077.2(UBE4A):c.2412+21_2412+23del variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 999,732 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
NM_001204077.2 splice_donor_5th_base, 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE4A | NM_001204077.2 | c.2412+21_2412+23del | splice_donor_5th_base_variant, intron_variant | ENST00000252108.8 | |||
LOC100131626 | NR_046370.1 | n.232-3443_232-3441del | intron_variant, non_coding_transcript_variant | ||||
UBE4A | NM_004788.4 | c.2433+21_2433+23del | splice_donor_5th_base_variant, intron_variant | ||||
LOC100131626 | NR_046369.1 | n.232-3390_232-3388del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE4A | ENST00000252108.8 | c.2412+21_2412+23del | splice_donor_5th_base_variant, intron_variant | 1 | NM_001204077.2 | P1 | |||
UBE4A | ENST00000431736.6 | c.2433+21_2433+23del | splice_donor_5th_base_variant, intron_variant | 1 | |||||
UBE4A | ENST00000545354.1 | c.828+21_828+23del | splice_donor_5th_base_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000340 AC: 27AN: 79454Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.116 AC: 9713AN: 83660Hom.: 0 AF XY: 0.116 AC XY: 5236AN XY: 45246
GnomAD4 exome AF: 0.0614 AC: 56500AN: 920288Hom.: 0 AF XY: 0.0619 AC XY: 28878AN XY: 466892
GnomAD4 genome AF: 0.000340 AC: 27AN: 79444Hom.: 0 Cov.: 29 AF XY: 0.000424 AC XY: 16AN XY: 37742
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at