chrX-154485914-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014235.5(UBL4A):c.220C>T(p.Leu74=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000912 in 1,096,995 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L74L) has been classified as Benign.
Frequency
Consequence
NM_014235.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBL4A | NM_014235.5 | c.220C>T | p.Leu74= | synonymous_variant | 3/4 | ENST00000369660.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBL4A | ENST00000369660.9 | c.220C>T | p.Leu74= | synonymous_variant | 3/4 | 1 | NM_014235.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 9.12e-7 AC: 1AN: 1096995Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 362679
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | UBL4A: PM2:Supporting, BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at