Variant 8-89784141-T-TAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_003821.6(RIPK2):c.1029+24_1029+25dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.028 ( 96 hom., cov: 0)

Exomes 𝑓: 0.012 ( 1 hom. )

Consequence

RIPK2
NM_003821.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.604

Variant links:

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]

RIPK2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
RIPK2	NM_003821.6 linkuse as main transcript	c.1029+24_1029+25dupAA	intron_variant	ENST00000220751.5	NP_003812.1	O43353-1A0A0S2Z4Z8
RIPK2	NM_001375360.1 linkuse as main transcript	c.618+24_618+25dupAA	intron_variant		NP_001362289.1
RIPK2	XM_011517357.3 linkuse as main transcript	c.516+24_516+25dupAA	intron_variant		XP_011515659.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIPK2	ENST00000220751.5 linkuse as main transcript	c.1029+24_1029+25dupAA		intron_variant		1	NM_003821.6	ENSP00000220751.4		O43353-1
RIPK2	ENST00000522965.1 linkuse as main transcript	n.668+24_668+25dupAA		intron_variant		1		ENSP00000429271.1		E7ERW9

Frequencies

GnomAD3 genomes

AF:

0.0280

AC:

2711

AN:

96892

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0548

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0181

Gnomad ASJ

AF:

0.0879

Gnomad EAS

AF:

0.00770

Gnomad SAS

AF:

0.0293

Gnomad FIN

AF:

0.00652

Gnomad MID

AF:

0.0182

Gnomad NFE

AF:

0.0164

Gnomad OTH

AF:

0.0282

GnomAD4 exome

AF:

0.0117

AC:

5341

AN:

457770

Hom.:

Cov.:

AF XY:

0.0122

AC XY:

2909

AN XY:

238220

show subpopulations

Gnomad4 AFR exome

AF:

0.0261

Gnomad4 AMR exome

AF:

0.0151

Gnomad4 ASJ exome

AF:

0.0247

Gnomad4 EAS exome

AF:

0.0159

Gnomad4 SAS exome

AF:

0.0277

Gnomad4 FIN exome

AF:

0.00746

Gnomad4 NFE exome

AF:

0.00952

Gnomad4 OTH exome

AF:

0.0127

GnomAD4 genome

AF:

0.0280

AC:

2715

AN:

96900

Hom.:

Cov.:

AF XY:

0.0285

AC XY:

1258

AN XY:

44134

show subpopulations

Gnomad4 AFR

AF:

0.0549

Gnomad4 AMR

AF:

0.0181

Gnomad4 ASJ

AF:

0.0879

Gnomad4 EAS

AF:

0.00771

Gnomad4 SAS

AF:

0.0295

Gnomad4 FIN

AF:

0.00652

Gnomad4 NFE

AF:

0.0164

Gnomad4 OTH

AF:

0.0287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over