8-89769900-A-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_003821.6(RIPK2):c.612A>T(p.Ser204=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,607,632 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 32 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 13 hom. )
Consequence
RIPK2
NM_003821.6 synonymous
NM_003821.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.99
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 8-89769900-A-T is Benign according to our data. Variant chr8-89769900-A-T is described in ClinVar as [Benign]. Clinvar id is 707947.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.99 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.01 (1521/151958) while in subpopulation AFR AF= 0.0343 (1424/41510). AF 95% confidence interval is 0.0328. There are 32 homozygotes in gnomad4. There are 677 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1520 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPK2 | NM_003821.6 | c.612A>T | p.Ser204= | synonymous_variant | 4/11 | ENST00000220751.5 | |
RIPK2 | NM_001375360.1 | c.201A>T | p.Ser67= | synonymous_variant | 3/10 | ||
RIPK2 | XM_011517357.3 | c.99A>T | p.Ser33= | synonymous_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPK2 | ENST00000220751.5 | c.612A>T | p.Ser204= | synonymous_variant | 4/11 | 1 | NM_003821.6 | P1 | |
RIPK2 | ENST00000522965.1 | c.*251A>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0100 AC: 1520AN: 151840Hom.: 32 Cov.: 32
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GnomAD3 exomes AF: 0.00260 AC: 642AN: 246756Hom.: 8 AF XY: 0.00192 AC XY: 257AN XY: 133636
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GnomAD4 exome AF: 0.00110 AC: 1595AN: 1455674Hom.: 13 Cov.: 31 AF XY: 0.000958 AC XY: 694AN XY: 724156
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GnomAD4 genome ? AF: 0.0100 AC: 1521AN: 151958Hom.: 32 Cov.: 32 AF XY: 0.00911 AC XY: 677AN XY: 74306
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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 | Invitae | May 31, 2018 | - - |
Computational 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