19-55401578-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014501.3(UBE2S):āc.527A>Cā(p.Glu176Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 1,606,250 control chromosomes in the GnomAD database, including 4,972 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_014501.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE2S | NM_014501.3 | c.527A>C | p.Glu176Ala | missense_variant | 4/4 | ENST00000264552.14 | |
RPL28 | NM_001363697.1 | c.325-1365T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE2S | ENST00000264552.14 | c.527A>C | p.Glu176Ala | missense_variant | 4/4 | 1 | NM_014501.3 | P1 | |
RPL28 | ENST00000560055.5 | c.325-1365T>G | intron_variant | 3 | |||||
UBE2S | ENST00000587845.5 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0665 AC: 10120AN: 152082Hom.: 407 Cov.: 32
GnomAD3 exomes AF: 0.0528 AC: 12341AN: 233570Hom.: 441 AF XY: 0.0516 AC XY: 6623AN XY: 128386
GnomAD4 exome AF: 0.0745 AC: 108386AN: 1454050Hom.: 4565 Cov.: 30 AF XY: 0.0729 AC XY: 52702AN XY: 723070
GnomAD4 genome ? AF: 0.0665 AC: 10119AN: 152200Hom.: 407 Cov.: 32 AF XY: 0.0645 AC XY: 4801AN XY: 74396
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