5-140114724-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_005859.5(PURA):c.543C>T(p.Gly181Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,612,930 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G181G) has been classified as Likely benign.
Frequency
Consequence
NM_005859.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PURA | ENST00000331327.5 | c.543C>T | p.Gly181Gly | synonymous_variant | Exon 1 of 1 | 6 | NM_005859.5 | ENSP00000332706.3 | ||
PURA | ENST00000651386.1 | c.543C>T | p.Gly181Gly | synonymous_variant | Exon 2 of 2 | ENSP00000499133.1 | ||||
PURA | ENST00000505703.2 | c.*224C>T | downstream_gene_variant | 3 | ENSP00000498560.1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000688 AC: 17AN: 247100Hom.: 0 AF XY: 0.0000521 AC XY: 7AN XY: 134316
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460560Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 726600
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74510
ClinVar
Submissions by phenotype
PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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PURA-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at