rs774603280
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_005859.5(PURA):c.270G>A(p.Glu90=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000744 in 1,612,818 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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
PURA
NM_005859.5 synonymous
NM_005859.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.74
Genes affected
PURA (HGNC:9701): (purine rich element binding protein A) This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 5-140114451-G-A is Benign according to our data. Variant chr5-140114451-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 542078.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PURA | NM_005859.5 | c.270G>A | p.Glu90= | synonymous_variant | 1/1 | ENST00000331327.5 | NP_005850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PURA | ENST00000331327.5 | c.270G>A | p.Glu90= | synonymous_variant | 1/1 | NM_005859.5 | ENSP00000332706 | P1 | ||
PURA | ENST00000651386.1 | c.270G>A | p.Glu90= | synonymous_variant | 2/2 | ENSP00000499133 | P1 | |||
PURA | ENST00000505703.2 | c.270G>A | p.Glu90= | synonymous_variant | 2/2 | 3 | ENSP00000498560 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000811 AC: 2AN: 246494Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134440
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460652Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 726660
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 15, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at