chr2-135780371-C-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_014607.4(UBXN4):āc.1374C>Gā(p.Ser458Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00071 in 1,613,540 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014607.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBXN4 | NM_014607.4 | c.1374C>G | p.Ser458Arg | missense_variant | 12/13 | ENST00000272638.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBXN4 | ENST00000272638.14 | c.1374C>G | p.Ser458Arg | missense_variant | 12/13 | 1 | NM_014607.4 | P1 | |
UBXN4 | ENST00000490163.5 | n.1073C>G | non_coding_transcript_exon_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00116 AC: 176AN: 152068Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00230 AC: 574AN: 249288Hom.: 11 AF XY: 0.00201 AC XY: 272AN XY: 135254
GnomAD4 exome AF: 0.000665 AC: 972AN: 1461352Hom.: 16 Cov.: 31 AF XY: 0.000666 AC XY: 484AN XY: 727002
GnomAD4 genome AF: 0.00114 AC: 173AN: 152188Hom.: 2 Cov.: 32 AF XY: 0.00120 AC XY: 89AN XY: 74406
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at