rs2307220
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002583.4(PAWR):c.*513T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,506 control chromosomes in the GnomAD database, including 15,397 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.35 ( 15396 hom., cov: 32)
Exomes 𝑓: 0.090 ( 1 hom. )
Consequence
PAWR
NM_002583.4 3_prime_UTR
NM_002583.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.235
Genes affected
PAWR (HGNC:8614): (pro-apoptotic WT1 regulator) This gene encodes a tumor suppressor protein that selectively induces apoptosis in cancer cells through intracellular and extracellular mechanisms. The intracellular mechanism involves the inhibition of pro-survival pathways and the activation of Fas-mediated apoptosis, while the extracellular mechanism involves the binding of a secreted form of this protein to glucose regulated protein 78 (GRP78) on the cell surface, which leads to activation of the extrinsic apoptotic pathway. This gene is located on the unstable human chromosomal 12q21 region and is often deleted or mutated different tumors. The encoded protein also plays an important role in the progression of age-related diseases. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAWR | NM_002583.4 | c.*513T>G | 3_prime_UTR_variant | 7/7 | ENST00000328827.9 | ||
PAWR | NM_001354732.2 | c.*513T>G | 3_prime_UTR_variant | 7/7 | |||
PAWR | XM_047428916.1 | c.*513T>G | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAWR | ENST00000328827.9 | c.*513T>G | 3_prime_UTR_variant | 7/7 | 1 | NM_002583.4 | P1 | ||
PAWR | ENST00000550603.1 | c.212+517T>G | intron_variant | 5 | |||||
PAWR | ENST00000548075.5 | n.503+517T>G | intron_variant, non_coding_transcript_variant | 4 | |||||
PAWR | ENST00000549050.1 | n.58-1813T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.347 AC: 52666AN: 151934Hom.: 15340 Cov.: 32
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GnomAD4 exome AF: 0.0903 AC: 41AN: 454Hom.: 1 Cov.: 0 AF XY: 0.0956 AC XY: 26AN XY: 272
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GnomAD4 genome ? AF: 0.347 AC: 52779AN: 152052Hom.: 15396 Cov.: 32 AF XY: 0.339 AC XY: 25221AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
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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