X-154485912-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_014235.5(UBL4A):c.222G>A(p.Leu74=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00605 in 1,209,497 control chromosomes in the GnomAD database, including 25 homozygotes. There are 2,320 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L74L) has been classified as Likely benign.
Frequency
Consequence
NM_014235.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBL4A | NM_014235.5 | c.222G>A | p.Leu74= | synonymous_variant | 3/4 | ENST00000369660.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBL4A | ENST00000369660.9 | c.222G>A | p.Leu74= | synonymous_variant | 3/4 | 1 | NM_014235.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00441 AC: 496AN: 112391Hom.: 3 Cov.: 24 AF XY: 0.00440 AC XY: 152AN XY: 34545
GnomAD3 exomes AF: 0.00549 AC: 990AN: 180366Hom.: 4 AF XY: 0.00519 AC XY: 342AN XY: 65906
GnomAD4 exome AF: 0.00622 AC: 6826AN: 1097054Hom.: 22 Cov.: 32 AF XY: 0.00598 AC XY: 2168AN XY: 362704
GnomAD4 genome AF: 0.00441 AC: 496AN: 112443Hom.: 3 Cov.: 24 AF XY: 0.00439 AC XY: 152AN XY: 34607
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at