rs281865548
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001143992.2(WRAP53):c.1192C>A(p.Arg398Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,598 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: not found (cov: 31)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
WRAP53
NM_001143992.2 synonymous
NM_001143992.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.05
Genes affected
WRAP53 (HGNC:25522): (WD repeat containing antisense to TP53) This gene encodes an essential component of the telomerase holoenzyme complex, a ribonucleoprotein complex required for telomere synthesis. This protein is enriched in Cajal bodies, nuclear sites of RNP processing that are important for telomerase function. It interacts with dyskerin, TERT and TERC, other components of active telomerase, and with small Cajal body RNAs (scaRNAs), which are involved in modifying splicing RNAs. This mRNA also functions as a p53 antisense transcript, that regulates endogenous p53 mRNA levels and further induction of p53 protein by targeting the 5' untranslated region of p53 mRNA. Alternatively spliced transcript variants which differ only in the 5' UTR have been found for this gene. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BP6
Variant 17-7702770-C-A is Benign according to our data. Variant chr17-7702770-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2884905.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.05 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| WRAP53 | NM_001143992.2 | c.1192C>A | p.Arg398Arg | synonymous_variant | Exon 9 of 11 | ENST00000396463.7 | NP_001137464.1 | |
| WRAP53 | NM_001143990.2 | c.1192C>A | p.Arg398Arg | synonymous_variant | Exon 9 of 11 | NP_001137462.1 | ||
| WRAP53 | NM_001143991.2 | c.1192C>A | p.Arg398Arg | synonymous_variant | Exon 9 of 11 | NP_001137463.1 | ||
| WRAP53 | NM_018081.2 | c.1192C>A | p.Arg398Arg | synonymous_variant | Exon 8 of 10 | NP_060551.2 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461598Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727104
GnomAD4 exome
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1461598
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33
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5
AN XY:
727104
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GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 02, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.