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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000220751.5(RIPK2):c.1029+2_1029+3insAAAA variant causes a splice region, 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 0.020 ( 47 hom., cov: 0)

Exomes 𝑓: 0.00078 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RIPK2
ENST00000220751.5 splice_region, 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 Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAdExome4 at 361 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
RIPK2	NM_003821.6 link	c.1029+22_1029+25dupAAAA	intron_variant	ENST00000220751.5	NP_003812.1	O43353-1A0A0S2Z4Z8
RIPK2	NM_001375360.1 link	c.618+22_618+25dupAAAA	intron_variant		NP_001362289.1
RIPK2	XM_011517357.3 link	c.516+22_516+25dupAAAA	intron_variant		XP_011515659.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RIPK2	ENST00000220751.5 link	c.1029+2_1029+3insAAAA		splice_region_variant, intron_variant		1	NM_003821.6	ENSP00000220751.4		O43353-1
RIPK2	ENST00000522965.1 link	n.668+2_668+3insAAAA		splice_region_variant, intron_variant		1		ENSP00000429271.1		E7ERW9

Frequencies

GnomAD3 genomes

AF:

0.0203

AC:

1968

AN:

97002

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0694

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0123

Gnomad ASJ

AF:

0.00572

Gnomad EAS

AF:

0.0448

Gnomad SAS

AF:

0.00854

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00901

Gnomad NFE

AF:

0.000792

Gnomad OTH

AF:

0.0218

GnomAD4 exome

AF:

0.000783

AC:

361

AN:

460938

Hom.:

Cov.:

AF XY:

0.000834

AC XY:

200

AN XY:

239884

show subpopulations

Gnomad4 AFR exome

AF:

0.00614

Gnomad4 AMR exome

AF:

0.00199

Gnomad4 ASJ exome

AF:

0.000877

Gnomad4 EAS exome

AF:

0.00467

Gnomad4 SAS exome

AF:

0.00274

Gnomad4 FIN exome

AF:

0.0000702

Gnomad4 NFE exome

AF:

0.000217

Gnomad4 OTH exome

AF:

0.00134

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0203

AC:

1974

AN:

97010

Hom.:

Cov.:

AF XY:

0.0213

AC XY:

939

AN XY:

44186

show subpopulations

Gnomad4 AFR

AF:

0.0695

Gnomad4 AMR

AF:

0.0122

Gnomad4 ASJ

AF:

0.00572

Gnomad4 EAS

AF:

0.0448

Gnomad4 SAS

AF:

0.00859

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000792

Gnomad4 OTH

AF:

0.0224

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