chr19-43665358-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002659.4(PLAUR):c.268G>A(p.Glu90Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000768 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E90G) has been classified as Uncertain significance.
Frequency
Consequence
NM_002659.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLAUR | NM_002659.4 | c.268G>A | p.Glu90Lys | missense_variant | 3/7 | ENST00000340093.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAUR | ENST00000340093.8 | c.268G>A | p.Glu90Lys | missense_variant | 3/7 | 1 | NM_002659.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151952Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251486Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135918
GnomAD4 exome AF: 0.0000800 AC: 117AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000715 AC XY: 52AN XY: 727238
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152070Hom.: 0 Cov.: 30 AF XY: 0.0000404 AC XY: 3AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 24, 2022 | The c.268G>A (p.E90K) alteration is located in exon 3 (coding exon 3) of the PLAUR gene. This alteration results from a G to A substitution at nucleotide position 268, causing the glutamic acid (E) at amino acid position 90 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at