Genetic Variant RIPK2:c.1029+14_1029+25delAAAAAAAAAAAA (chr8-89784141-TAAAAAAAAAAAA-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000220751.5(RIPK2):c.1029+3_1029+14delAAAAAAAAAAAA variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000287 in 558,308 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000010 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000033 ( 0 hom. )

Consequence

RIPK2
ENST00000220751.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.92

Publications

0 publications found

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:

PARAIL (HGNC:55545): (palmitic acid regulated anti-inflammatory lncRNA)

PARAIL links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAdExome4 at 15 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000220751.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPK2	NM_003821.6	MANE Select	c.1029+14_1029+25delAAAAAAAAAAAA		intron	N/A	NP_003812.1
	RIPK2	NM_001375360.1		c.618+14_618+25delAAAAAAAAAAAA		intron	N/A	NP_001362289.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RIPK2	ENST00000220751.5	TSL:1 MANE Select	c.1029+3_1029+14delAAAAAAAAAAAA	splice_region intron	N/A	ENSP00000220751.4
RIPK2	ENST00000522965.1	TSL:1	n.668+3_668+14delAAAAAAAAAAAA	splice_region intron	N/A	ENSP00000429271.1
RIPK2	ENST00000929530.1		c.1089+3_1089+14delAAAAAAAAAAAA	splice_region intron	N/A	ENSP00000599589.1

Frequencies

GnomAD3 genomes

AF:

0.0000103

AC:

AN:

97062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000193

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000325

AC:

AN:

461246

Hom.:

AF XY:

0.0000333

AC XY:

AN XY:

240042

show subpopulations

African (AFR)

AF:

0.000105

AC:

AN:

9518

American (AMR)

AF:

0.00

AC:

AN:

11044

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10276

East Asian (EAS)

AF:

0.000339

AC:

AN:

20672

South Asian (SAS)

AF:

0.00

AC:

AN:

25888

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28494

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1686

European-Non Finnish (NFE)

AF:

0.0000211

AC:

AN:

331314

Other (OTH)

AF:

0.00

AC:

AN:

22354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.402

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000103

AC:

AN:

97062

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

44190

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23440

American (AMR)

AF:

0.00

AC:

AN:

8908

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2796

East Asian (EAS)

AF:

0.00

AC:

AN:

2860

South Asian (SAS)

AF:

0.00

AC:

AN:

2458

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

222

European-Non Finnish (NFE)

AF:

0.0000193

AC:

AN:

51766

Other (OTH)

AF:

0.00

AC:

AN:

1282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.9

Splicing

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

Publications

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8-89784141-TAAAAAAAAAAAAAAAA-TAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over