rs724165
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006871.4(RIPK3):c.1275+63C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 1,603,026 control chromosomes in the GnomAD database, including 240,554 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 0.44 ( 17229 hom., cov: 32)
Exomes 𝑓: 0.54 ( 223325 hom. )
Consequence
RIPK3
NM_006871.4 intron
NM_006871.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.172
Genes affected
RIPK3 (HGNC:10021): (receptor interacting serine/threonine kinase 3) The product of this gene is a member of the receptor-interacting protein (RIP) family of serine/threonine protein kinases, and contains a C-terminal domain unique from other RIP family members. The encoded protein is predominantly localized to the cytoplasm, and can undergo nucleocytoplasmic shuttling dependent on novel nuclear localization and export signals. It is a component of the tumor necrosis factor (TNF) receptor-I signaling complex, and can induce apoptosis and weakly activate the NF-kappaB transcription factor. [provided by RefSeq, Jul 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=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPK3 | NM_006871.4 | c.1275+63C>T | intron_variant | ENST00000216274.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPK3 | ENST00000216274.10 | c.1275+63C>T | intron_variant | 1 | NM_006871.4 | P1 | |||
RIPK3 | ENST00000554756.1 | c.*617+63C>T | intron_variant, NMD_transcript_variant | 1 | |||||
RIPK3 | ENST00000554569.1 | c.317+63C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.439 AC: 66650AN: 151918Hom.: 17227 Cov.: 32
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GnomAD4 exome AF: 0.544 AC: 789038AN: 1450990Hom.: 223325 Cov.: 39 AF XY: 0.542 AC XY: 390486AN XY: 720642
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GnomAD4 genome ? AF: 0.439 AC: 66668AN: 152036Hom.: 17229 Cov.: 32 AF XY: 0.436 AC XY: 32391AN XY: 74312
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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