1-156041653-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_020131.5(UBQLN4):āc.1485A>Gā(p.Ile495Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 1,565,318 control chromosomes in the GnomAD database, including 280,130 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020131.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBQLN4 | NM_020131.5 | c.1485A>G | p.Ile495Met | missense_variant | 10/11 | ENST00000368309.4 | |
UBQLN4 | NM_001304342.2 | c.1425A>G | p.Ile475Met | missense_variant | 10/11 | ||
UBQLN4 | XM_024448469.2 | c.1485A>G | p.Ile495Met | missense_variant | 10/11 | ||
UBQLN4 | XM_047425666.1 | c.951A>G | p.Ile317Met | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBQLN4 | ENST00000368309.4 | c.1485A>G | p.Ile495Met | missense_variant | 10/11 | 1 | NM_020131.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.542 AC: 82370AN: 151898Hom.: 23377 Cov.: 33
GnomAD3 exomes AF: 0.529 AC: 100560AN: 189974Hom.: 28165 AF XY: 0.537 AC XY: 55073AN XY: 102564
GnomAD4 exome AF: 0.596 AC: 841922AN: 1413302Hom.: 256733 Cov.: 58 AF XY: 0.595 AC XY: 415849AN XY: 699304
GnomAD4 genome AF: 0.542 AC: 82419AN: 152016Hom.: 23397 Cov.: 33 AF XY: 0.539 AC XY: 40032AN XY: 74314
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at