rs6966
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006663.4(PPP1R13L):c.*486A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 156,236 control chromosomes in the GnomAD database, including 10,171 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 0.30 ( 10081 hom., cov: 31)
Exomes 𝑓: 0.17 ( 90 hom. )
Consequence
PPP1R13L
NM_006663.4 3_prime_UTR
NM_006663.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.256
Genes affected
PPP1R13L (HGNC:18838): (protein phosphatase 1 regulatory subunit 13 like) IASPP is one of the most evolutionarily conserved inhibitors of p53 (TP53; MIM 191170), whereas ASPP1 (MIM 606455) and ASPP2 (MIM 602143) are activators of p53.[supplied by OMIM, Mar 2008]
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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=-0.75).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R13L | NM_006663.4 | c.*486A>T | 3_prime_UTR_variant | 13/13 | ENST00000360957.10 | ||
PPP1R13L | NM_001142502.2 | c.*486A>T | 3_prime_UTR_variant | 13/13 | |||
PPP1R13L | XM_017026177.2 | c.*486A>T | 3_prime_UTR_variant | 14/14 | |||
PPP1R13L | XM_017026178.2 | c.*486A>T | 3_prime_UTR_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R13L | ENST00000360957.10 | c.*486A>T | 3_prime_UTR_variant | 13/13 | 1 | NM_006663.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.304 AC: 46159AN: 151940Hom.: 10054 Cov.: 31
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GnomAD3 exomes AF: 0.176 AC: 1037AN: 5878Hom.: 112 AF XY: 0.155 AC XY: 431AN XY: 2772
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GnomAD4 exome AF: 0.169 AC: 706AN: 4178Hom.: 90 Cov.: 0 AF XY: 0.173 AC XY: 375AN XY: 2170
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GnomAD4 genome ? AF: 0.304 AC: 46236AN: 152058Hom.: 10081 Cov.: 31 AF XY: 0.303 AC XY: 22519AN XY: 74328
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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