8-89784141-T-TA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_003821.6(RIPK2):c.1029+25dup variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.32 ( 5283 hom., cov: 0)
Exomes 𝑓: 0.075 ( 11 hom. )
Consequence
RIPK2
NM_003821.6 splice_region, intron
NM_003821.6 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.604
Genes affected
RIPK2 (HGNC:10020): (receptor interacting serine/threonine kinase 2) This gene encodes a member of the receptor-interacting protein (RIP) family of serine/threonine protein kinases. The encoded protein contains a C-terminal caspase activation and recruitment domain (CARD), and is a component of signaling complexes in both the innate and adaptive immune pathways. It is a potent activator of NF-kappaB and inducer of apoptosis in response to various stimuli. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 8-89784141-T-TA is Benign according to our data. Variant chr8-89784141-T-TA is described in ClinVar as [Benign]. Clinvar id is 2867178.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPK2 | NM_003821.6 | c.1029+25dup | splice_region_variant, intron_variant | ENST00000220751.5 | |||
RIPK2 | NM_001375360.1 | c.618+25dup | splice_region_variant, intron_variant | ||||
RIPK2 | XM_011517357.3 | c.516+25dup | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPK2 | ENST00000220751.5 | c.1029+25dup | splice_region_variant, intron_variant | 1 | NM_003821.6 | P1 | |||
RIPK2 | ENST00000522965.1 | c.*668+25dup | splice_region_variant, intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.324 AC: 31322AN: 96572Hom.: 5282 Cov.: 0
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GnomAD3 exomes AF: 0.0323 AC: 925AN: 28604Hom.: 19 AF XY: 0.0305 AC XY: 463AN XY: 15204
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GnomAD4 exome AF: 0.0750 AC: 33709AN: 449438Hom.: 11 Cov.: 0 AF XY: 0.0754 AC XY: 17632AN XY: 233904
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GnomAD4 genome AF: 0.324 AC: 31320AN: 96586Hom.: 5283 Cov.: 0 AF XY: 0.320 AC XY: 14085AN XY: 43948
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 08, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at