7-129857572-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_003344.4(UBE2H):c.246-9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,609,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003344.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBE2H | NM_003344.4 | c.246-9C>T | intron_variant | Intron 4 of 6 | ENST00000355621.8 | NP_003335.1 | ||
UBE2H | NM_182697.3 | c.206-18237C>T | intron_variant | Intron 3 of 4 | NP_874356.1 | |||
UBE2H | NM_001202498.2 | c.36-9C>T | intron_variant | Intron 4 of 6 | NP_001189427.1 | |||
UBE2H | XM_047420796.1 | c.36-9C>T | intron_variant | Intron 5 of 7 | XP_047276752.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000609 AC: 15AN: 246208Hom.: 0 AF XY: 0.0000526 AC XY: 7AN XY: 133078
GnomAD4 exome AF: 0.0000220 AC: 32AN: 1457630Hom.: 0 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 725006
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
UBE2H-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at